3-157966858-C-T

Variant names:

• chr3-157966858-C-T
• rs9290011
• ENST00000651134.1:n.570-4793G>A

Variant summary

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

The ENST00000651134.1(ENSG00000242536):​n.570-4793G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,054 control chromosomes in the GnomAD database, including 12,354 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 0.39 (12354 hom., cov: 32)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 4 publications found

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000242536	ENST00000651134.1	n.570-4793G>A		intron_variant	Intron 4 of 12

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59896 AN: 151936 Hom.: 12346 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.394 AC: 59936 AN: 152054 Hom.: 12354 Cov.: 32 AF XY: 0.395 AC XY: 29328 AN XY: 74328

African (AFR) AF: 0.275 AC: 11425 AN: 41484

American (AMR) AF: 0.383 AC: 5849 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1656 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2113 AN: 5162

South Asian (SAS) AF: 0.527 AC: 2544 AN: 4824

European-Finnish (FIN) AF: 0.420 AC: 4428 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30774 AN: 67966

Other (OTH) AF: 0.391 AC: 827 AN: 2114

Alfa AF: 0.336 Hom.: 1366

Bravo AF: 0.385

Asia WGS AF: 0.506 AC: 1761 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	2.7
DANN	Benign	0.56
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs9290011; hg19: chr3-157684647;