chr3-192042662-G-A

Variant names:

• chr3-192042662-G-A
• rs1491520

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 0.163 in 151,942 control chromosomes in the GnomAD database, including 2,266 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 0.16 (2266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24757 AN: 151824 Hom.: 2267 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.163 AC: 24770 AN: 151942 Hom.: 2266 Cov.: 31 AF XY: 0.160 AC XY: 11878 AN XY: 74286

African (AFR) AF: 0.243 AC: 10053 AN: 41382

American (AMR) AF: 0.121 AC: 1854 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3464

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5166

South Asian (SAS) AF: 0.140 AC: 675 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1315 AN: 10560

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8761 AN: 67958

Other (OTH) AF: 0.142 AC: 299 AN: 2112

Alfa AF: 0.140 Hom.: 6589

Bravo AF: 0.167

Asia WGS AF: 0.176 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1491520; hg19: chr3-191760451;