18-45737582-C-T

Variant names:

• chr18-45737582-C-T
• rs10853535
• NM_015865.7:c.663+934C>T

Variant summary

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

The NM_015865.7(SLC14A1):​c.663+934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,014 control chromosomes in the GnomAD database, including 29,019 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 (29019 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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.663+934C>T		intron	N/A	NP_056949.4	Q13336-1
	SLC14A1	NM_001128588.4		c.831+934C>T		intron	N/A	NP_001122060.3	Q13336-2
	SLC14A1	NM_001146037.1		c.831+934C>T		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.663+934C>T		intron	N/A	ENSP00000318546.4	Q13336-1
	SLC14A1	ENST00000586142.5	TSL:1	c.663+934C>T		intron	N/A	ENSP00000470476.1	Q13336-1
	SLC14A1	ENST00000589700.5	TSL:1	c.663+934C>T		intron	N/A	ENSP00000465044.1	E9NSU1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92939 AN: 151894 Hom.: 28992 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.612 AC: 93017 AN: 152012 Hom.: 29019 Cov.: 33 AF XY: 0.615 AC XY: 45717 AN XY: 74318

African (AFR) AF: 0.652 AC: 27020 AN: 41450

American (AMR) AF: 0.688 AC: 10526 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3468

East Asian (EAS) AF: 0.928 AC: 4814 AN: 5188

South Asian (SAS) AF: 0.678 AC: 3269 AN: 4820

European-Finnish (FIN) AF: 0.593 AC: 6244 AN: 10534

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37567 AN: 67952

Other (OTH) AF: 0.594 AC: 1250 AN: 2104

Alfa AF: 0.583 Hom.: 48501

Bravo AF: 0.620

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.20
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: rs10853535; hg19: chr18-43317547;