rs692899

chr18-45736305-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.471-151T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 718,282 control chromosomes in the GnomAD database, including 37,703 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 0.26 (6456 hom., cov: 32)
  • Exomes 𝑓: 0.32 (31247 hom.)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A1	NM_015865.7	c.471-151T>C		intron_variant		ENST00000321925.9
LOC105372093	XR_935423.3	n.826+1161A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A1	ENST00000321925.9	c.471-151T>C		intron_variant		1	NM_015865.7	P1
	ENST00000589510.5	n.160+1161A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39093 AN: 152040 Hom.: 6454 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.283

GnomAD4 exome AF: 0.319 AC: 180413 AN: 566124 Hom.: 31247 AF XY: 0.321 AC XY: 97405 AN XY: 303316

Gnomad4 AFR exome AF: 0.0700

Gnomad4 AMR exome AF: 0.199

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.0653

Gnomad4 SAS exome AF: 0.295

Gnomad4 FIN exome AF: 0.326

Gnomad4 NFE exome AF: 0.366

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.257 AC: 39095 AN: 152158 Hom.: 6456 Cov.: 32 AF XY: 0.257 AC XY: 19134 AN XY: 74368

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0718

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.286

Alfa AF: 0.322 Hom.: 4127

Bravo AF: 0.239

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.3
Dann	Benign	0.74

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: rs692899; hg19: chr18-43316270;