chr18-45737317-T-C

Variant names:

• chr18-45737317-T-C
• rs10775480
• NM_015865.7:c.663+669T>C

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+669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 153,098 control chromosomes in the GnomAD database, including 29,102 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 (28950 hom., cov: 33)
  • Exomes 𝑓: 0.57 (152 hom.)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 23 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]

ENSG00000288545 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.663+669T>C		intron_variant	Intron 6 of 9	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.663+669T>C		intron_variant	Intron 6 of 9	1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92860 AN: 152034 Hom.: 28923 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.687

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: 0.595

GnomAD4 exome AF: 0.571 AC: 540 AN: 946 Hom.: 152 AF XY: 0.552 AC XY: 267 AN XY: 484

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.667 AC: 116 AN: 174

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.875 AC: 7 AN: 8

South Asian (SAS) AF: 0.700 AC: 35 AN: 50

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.538 AC: 367 AN: 682

Other (OTH) AF: 0.467 AC: 14 AN: 30

GnomAD4 genome AF: 0.611 AC: 92936 AN: 152152 Hom.: 28950 Cov.: 33 AF XY: 0.614 AC XY: 45684 AN XY: 74394

African (AFR) AF: 0.648 AC: 26892 AN: 41468

American (AMR) AF: 0.688 AC: 10522 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3466

East Asian (EAS) AF: 0.928 AC: 4816 AN: 5190

South Asian (SAS) AF: 0.678 AC: 3263 AN: 4812

European-Finnish (FIN) AF: 0.593 AC: 6283 AN: 10594

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

European-Non Finnish (NFE) AF: 0.553 AC: 37583 AN: 68008

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.578 Hom.: 43774

Bravo AF: 0.619

Asia WGS AF: 0.770 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.46
PhyloP100		0.073
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: rs10775480; hg19: chr18-43317282;