chr3-162027101-G-C

Variant names:

• chr3-162027101-G-C
• rs4453857

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 0.0204 in 151,774 control chromosomes in the GnomAD database, including 157 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 0.020 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 1 publications found

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 = 0.172 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

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3107 AN: 151656 Hom.: 159 Cov.: 32

Gnomad AFR AF: 0.00462

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.0191

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0204 AC: 3096 AN: 151774 Hom.: 157 Cov.: 32 AF XY: 0.0243 AC XY: 1801 AN XY: 74164

African (AFR) AF: 0.00461 AC: 191 AN: 41474

American (AMR) AF: 0.0283 AC: 431 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0191 AC: 66 AN: 3464

East Asian (EAS) AF: 0.138 AC: 701 AN: 5092

South Asian (SAS) AF: 0.182 AC: 879 AN: 4822

European-Finnish (FIN) AF: 0.000754 AC: 8 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 749 AN: 67790

Other (OTH) AF: 0.0303 AC: 64 AN: 2110

Alfa AF: 0.0129 Hom.: 10

Bravo AF: 0.0190

Asia WGS AF: 0.124 AC: 433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.75
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4453857; hg19: chr3-161744889;