18-45737582-C-T

Variant summary

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

The NM_015865.7(SLC14A1):c.663+934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,014 control chromosomes in the GnomAD database, including 29,019 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 (29019 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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=-0.9).
• 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+934C>T		intron_variant		ENST00000321925.9
LOC105372093	XR_935423.3	n.710G>A		non_coding_transcript_exon_variant	6/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A1	ENST00000321925.9	c.663+934C>T		intron_variant		1	NM_015865.7	P1
	ENST00000589510.5	n.44G>A		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92939 AN: 151894 Hom.: 28992 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.688

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: 0.596

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.612 AC: 93017 AN: 152012 Hom.: 29019 Cov.: 33 AF XY: 0.615 AC XY: 45717 AN XY: 74318

Gnomad4 AFR AF: 0.652

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: 0.594

Alfa AF: 0.586 Hom.: 12398

Bravo AF: 0.620

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	-0.90
Cadd	Benign	1.8
Dann	Benign	0.56

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: rs10853535; hg19: chr18-43317547;