3-157818394-C-T

Position:

• chr3-157818394-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651134.1(ENSG00000242536):​n.1312-3500G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,054 control chromosomes in the GnomAD database, including 2,758 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 0.19 (2758 hom., cov: 32)
• Consequence: ENST00000651134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651134.1	n.1312-3500G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28659 AN: 151936 Hom.: 2760 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.189 AC: 28665 AN: 152054 Hom.: 2758 Cov.: 32 AF XY: 0.193 AC XY: 14330 AN XY: 74318

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.176

Alfa AF: 0.184 Hom.: 5076

Bravo AF: 0.190

Asia WGS AF: 0.199 AC: 692 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	0.64
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16828352; hg19: chr3-157536183; COSMIC: COSV66118036;