rs113578396

Variant names:

• chr18-45730348-G-A
• rs113578396
• NM_015865.7:c.28G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-45730348-G-A
• chr18-45730348-G-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_015865.7(SLC14A1):​c.28G>A​(p.Val10Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 1,613,198 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (68 hom., cov: 32)
  • Exomes 𝑓: 0.0028 (84 hom.)
• Consequence: SLC14A1 NM_015865.7 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.13
• Publications: 8 publications found

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

SLC14A1 Gene-Disease associations (from GenCC):

• blood group, kidd system

  Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia

ENSG00000288545 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0014895201).
• BP6: Variant 18-45730348-G-A is Benign according to our data. Variant chr18-45730348-G-A is described in ClinVar as Benign. ClinVar VariationId is 773341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.056 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015865.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	NM_015865.7	MANE Select	c.28G>A	p.Val10Met	missense	Exon 3 of 10	NP_056949.4	Q13336-1
	SLC14A1	NM_001128588.4		c.196G>A	p.Val66Met	missense	Exon 4 of 11	NP_001122060.3	Q13336-2
	SLC14A1	NM_001146037.1		c.196G>A	p.Val66Met	missense	Exon 2 of 9	NP_001139509.1	Q13336-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	ENST00000321925.9	TSL:1 MANE Select	c.28G>A	p.Val10Met	missense	Exon 3 of 10	ENSP00000318546.4	Q13336-1
	SLC14A1	ENST00000586142.5	TSL:1	c.28G>A	p.Val10Met	missense	Exon 1 of 8	ENSP00000470476.1	Q13336-1
	SLC14A1	ENST00000589700.5	TSL:1	c.28G>A	p.Val10Met	missense	Exon 1 of 7	ENSP00000465044.1	E9NSU1

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2719 AN: 151730 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00128

Gnomad OTH AF: 0.0124

GnomAD2 exomes AF: 0.00569 AC: 1430 AN: 251288 AF XY: 0.00451

Gnomad AFR exome AF: 0.0587

Gnomad AMR exome AF: 0.00587

Gnomad ASJ exome AF: 0.00169

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00183

Gnomad OTH exome AF: 0.00522

GnomAD4 exome AF: 0.00284 AC: 4156 AN: 1461352 Hom.: 84 Cov.: 31 AF XY: 0.00265 AC XY: 1924 AN XY: 727004

African (AFR) AF: 0.0611 AC: 2026 AN: 33156

American (AMR) AF: 0.00669 AC: 299 AN: 44674

Ashkenazi Jewish (ASJ) AF: 0.00157 AC: 41 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39688

South Asian (SAS) AF: 0.000626 AC: 54 AN: 86252

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53420

Middle Eastern (MID) AF: 0.0162 AC: 93 AN: 5748

European-Non Finnish (NFE) AF: 0.00105 AC: 1166 AN: 1111920

Other (OTH) AF: 0.00789 AC: 476 AN: 60358

GnomAD4 genome AF: 0.0179 AC: 2723 AN: 151846 Hom.: 68 Cov.: 32 AF XY: 0.0177 AC XY: 1311 AN XY: 74260

African (AFR) AF: 0.0580 AC: 2385 AN: 41132

American (AMR) AF: 0.0135 AC: 207 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4826

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00126 AC: 86 AN: 68018

Other (OTH) AF: 0.0123 AC: 26 AN: 2112

Alfa AF: 0.00688 Hom.: 55

Bravo AF: 0.0210

TwinsUK AF: 0.00108 AC: 4

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.0515 AC: 227

ESP6500EA AF: 0.00105 AC: 9

ExAC AF: 0.00656 AC: 796

EpiCase AF: 0.00289

EpiControl AF: 0.00279

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Benign	-0.68	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.20
DANN	Benign	0.77
DEOGEN2	Benign	0.049	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.0086	N
LIST_S2	Benign	0.61	T
MetaRNN	Benign	0.0015	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.36	N
PhyloP100		-2.1
PrimateAI	Benign	0.32	T
PROVEAN	Benign	-0.44	N
REVEL	Benign	0.078
Sift	Benign	0.25	T
Sift4G	Benign	0.43	T
Polyphen		0.0030	B
Vest4		0.035
MVP		0.030
MPC		0.11
ClinPred		0.0056	T
GERP RS		-11
PromoterAI		-0.0020	Neutral
Varity_R		0.040
gMVP		0.085
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs113578396; hg19: chr18-43310313;