NM_015865.7:c.471-151T>C

Variant names:

• chr18-45736305-T-C
• rs692899
• NM_015865.7:c.471-151T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000288545 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.471-151T>C		intron_variant	Intron 5 of 9	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.471-151T>C		intron_variant	Intron 5 of 9	1	NM_015865.7	ENSP00000318546.4

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

African (AFR) AF: 0.0700 AC: 1074 AN: 15346

American (AMR) AF: 0.199 AC: 6233 AN: 31260

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 6934 AN: 18502

East Asian (EAS) AF: 0.0653 AC: 2119 AN: 32438

South Asian (SAS) AF: 0.295 AC: 17191 AN: 58216

European-Finnish (FIN) AF: 0.326 AC: 13031 AN: 39992

Middle Eastern (MID) AF: 0.373 AC: 874 AN: 2346

European-Non Finnish (NFE) AF: 0.366 AC: 123555 AN: 337516

Other (OTH) AF: 0.308 AC: 9402 AN: 30508

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

African (AFR) AF: 0.0689 AC: 2861 AN: 41546

American (AMR) AF: 0.226 AC: 3462 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3470

East Asian (EAS) AF: 0.0718 AC: 372 AN: 5180

South Asian (SAS) AF: 0.300 AC: 1443 AN: 4816

European-Finnish (FIN) AF: 0.330 AC: 3488 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24898 AN: 67970

Other (OTH) AF: 0.286 AC: 606 AN: 2116

Alfa AF: 0.281 Hom.: 5546

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
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs692899; hg19: chr18-43316270;