rs471976

Variant names:

• chr3-170731148-C-T
• rs471976
• ENST00000486975.1:c.*44+22954C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486975.1(ENSG00000285218):​c.*44+22954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,998 control chromosomes in the GnomAD database, including 6,331 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 0.28 (6331 hom., cov: 32)
• Consequence: ENSG00000285218 ENST00000486975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 1 publications found

Genes affected

ENSG00000285218 (HGNC:):

SLC7A14-AS1 (HGNC:54092): (SLC7A14 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A14-AS1	NR_135556.1	n.766+1453C>T		intron_variant	Intron 5 of 5
LOC124906302	XR_007096159.1	n.268+2535G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285218	ENST00000486975.1	c.*44+22954C>T		intron_variant	Intron 3 of 3	2		ENSP00000417434.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42102 AN: 151880 Hom.: 6326 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.277 AC: 42125 AN: 151998 Hom.: 6331 Cov.: 32 AF XY: 0.284 AC XY: 21118 AN XY: 74286

African (AFR) AF: 0.317 AC: 13135 AN: 41434

American (AMR) AF: 0.297 AC: 4542 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3058 AN: 5156

South Asian (SAS) AF: 0.360 AC: 1733 AN: 4808

European-Finnish (FIN) AF: 0.305 AC: 3221 AN: 10548

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14690 AN: 67986

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.261 Hom.: 1077

Bravo AF: 0.281

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		0.081
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs471976; hg19: chr3-170448937;