rs11082469

Positions:

• chr18-45741304-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC105372093 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.946+1642A>G		intron_variant		ENST00000321925.9	NP_056949.4
LOC105372093	XR_935423.3	n.698-3710T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.946+1642A>G		intron_variant		1	NM_015865.7	ENSP00000318546	P1

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.455

Alfa AF: 0.475 Hom.: 22589

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11082469; hg19: chr18-43321269;