3-156582935-C-T

Variant names:

• chr3-156582935-C-T
• rs1510272

Variant summary

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

The variant allele was found at a frequency of 0.257 in 151,970 control chromosomes in the GnomAD database, including 5,170 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 (5170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38977 AN: 151852 Hom.: 5152 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.257 AC: 39023 AN: 151970 Hom.: 5170 Cov.: 32 AF XY: 0.259 AC XY: 19264 AN XY: 74258

African (AFR) AF: 0.208 AC: 8624 AN: 41448

American (AMR) AF: 0.267 AC: 4072 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5164

South Asian (SAS) AF: 0.323 AC: 1556 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3275 AN: 10538

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18150 AN: 67958

Other (OTH) AF: 0.267 AC: 564 AN: 2112

Alfa AF: 0.264 Hom.: 19092

Bravo AF: 0.250

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1510272; hg19: chr3-156300724;