3-170737156-T-C

Variant names:

• chr3-170737156-T-C
• rs577098
• ENST00000486975.1:c.*44+28962T>C

Variant summary

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

The ENST00000486975.1(ENSG00000285218):​c.*44+28962T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,554 control chromosomes in the GnomAD database, including 6,364 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 (6364 hom., cov: 30)
• Consequence: ENSG00000285218 ENST00000486975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A14-AS1	NR_135556.1	n.766+7461T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285218	ENST00000486975.1	c.*44+28962T>C		intron_variant	Intron 3 of 3	2		ENSP00000417434.1
SLC7A14-AS1	ENST00000480067.1	n.769+7461T>C		intron_variant	Intron 5 of 5	1
SLC7A14-AS1	ENST00000644993.1	n.293+28962T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42128 AN: 151440 Hom.: 6359 Cov.: 30

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.310

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: 0.278 AC: 42150 AN: 151554 Hom.: 6364 Cov.: 30 AF XY: 0.285 AC XY: 21104 AN XY: 74016

African (AFR) AF: 0.320 AC: 13211 AN: 41300

American (AMR) AF: 0.299 AC: 4548 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3466

East Asian (EAS) AF: 0.595 AC: 3065 AN: 5148

South Asian (SAS) AF: 0.361 AC: 1724 AN: 4778

European-Finnish (FIN) AF: 0.305 AC: 3196 AN: 10462

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14659 AN: 67862

Other (OTH) AF: 0.270 AC: 567 AN: 2100

Alfa AF: 0.110 Hom.: 181

Bravo AF: 0.283

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.061
PhyloP100		-1.4
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: rs577098; hg19: chr3-170454945; COSMIC: COSV72116348; COSMIC: COSV72116348;