rs11082469

Variant names:

• chr18-45741304-A-G
• rs11082469
• NM_015865.7:c.946+1642A>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.946+1642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,060 control chromosomes in the GnomAD database, including 14,975 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 0.44 (14975 hom., cov: 33)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.946+1642A>G		intron_variant	Intron 8 of 9	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.946+1642A>G		intron_variant	Intron 8 of 9	1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66421 AN: 151942 Hom.: 14977 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.437 AC: 66431 AN: 152060 Hom.: 14975 Cov.: 33 AF XY: 0.435 AC XY: 32310 AN XY: 74324

African (AFR) AF: 0.325 AC: 13494 AN: 41476

American (AMR) AF: 0.490 AC: 7494 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3472

East Asian (EAS) AF: 0.522 AC: 2695 AN: 5158

South Asian (SAS) AF: 0.407 AC: 1961 AN: 4816

European-Finnish (FIN) AF: 0.479 AC: 5056 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32814 AN: 67980

Other (OTH) AF: 0.455 AC: 960 AN: 2112

Alfa AF: 0.462 Hom.: 31376

Bravo AF: 0.435

Asia WGS AF: 0.434 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.79
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: rs11082469; hg19: chr18-43321269;