18-45749233-A-G

Variant names:

• chr18-45749233-A-G
• rs16809
• NM_015865.7:c.997-545A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015865.7(SLC14A1):​c.997-545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,914 control chromosomes in the GnomAD database, including 29,250 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (29250 hom., cov: 31)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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.997-545A>G		intron	N/A	NP_056949.4	Q13336-1
	SLC14A1	NM_001128588.4		c.1165-545A>G		intron	N/A	NP_001122060.3	Q13336-2
	SLC14A1	NM_001146037.1		c.1165-545A>G		intron	N/A	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.997-545A>G		intron	N/A	ENSP00000318546.4	Q13336-1
	SLC14A1	ENST00000586142.5	TSL:1	c.997-545A>G		intron	N/A	ENSP00000470476.1	Q13336-1
	SLC14A1	ENST00000589700.5	TSL:1	c.849-545A>G		intron	N/A	ENSP00000465044.1	E9NSU1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93093 AN: 151796 Hom.: 29239 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.620

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93141 AN: 151914 Hom.: 29250 Cov.: 31 AF XY: 0.616 AC XY: 45746 AN XY: 74242

African (AFR) AF: 0.502 AC: 20774 AN: 41406

American (AMR) AF: 0.708 AC: 10813 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3468

East Asian (EAS) AF: 0.929 AC: 4794 AN: 5160

South Asian (SAS) AF: 0.689 AC: 3316 AN: 4812

European-Finnish (FIN) AF: 0.670 AC: 7057 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42435 AN: 67952

Other (OTH) AF: 0.616 AC: 1298 AN: 2106

Alfa AF: 0.616 Hom.: 26343

Bravo AF: 0.611

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.60
PhyloP100		-0.58
Mutation Taster		=100/0	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: rs16809; hg19: chr18-43329198;