18-45737001-T-C

Position:

• chr18-45737001-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015865.7(SLC14A1):​c.663+353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,418 control chromosomes in the GnomAD database, including 28,715 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 (28715 hom., cov: 30)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.663+353T>C		intron_variant		ENST00000321925.9	NP_056949.4
LOC105372093	XR_935423.3	n.826+465A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.663+353T>C		intron_variant		1	NM_015865.7	ENSP00000318546	P1
	ENST00000589510.5	n.160+465A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92268 AN: 151300 Hom.: 28688 Cov.: 30

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.610 AC: 92344 AN: 151418 Hom.: 28715 Cov.: 30 AF XY: 0.613 AC XY: 45274 AN XY: 73896

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.594

Alfa AF: 0.566 Hom.: 32782

Bravo AF: 0.619

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.73

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: rs7238033; hg19: chr18-43316966;