3-156582935-C-T

Position:

• chr3-156582935-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.267

Alfa AF: 0.267 Hom.: 9203

Bravo AF: 0.250

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510272; hg19: chr3-156300724;