18-45737317-T-C

Position:

• chr18-45737317-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+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

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=-0.92).
• 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/exons	MANE	UniProt
SLC14A1	NM_015865.7	c.663+669T>C		intron_variant		ENST00000321925.9
LOC105372093	XR_935423.3	n.826+149A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A1	ENST00000321925.9	c.663+669T>C		intron_variant		1	NM_015865.7	P1
	ENST00000589510.5	n.160+149A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.875

Gnomad4 SAS exome AF: 0.700

Gnomad4 NFE exome AF: 0.538

Gnomad4 OTH exome AF: 0.467

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

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.593

Alfa AF: 0.581 Hom.: 10617

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

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: rs10775480; hg19: chr18-43317282;