3-161788092-T-G

Variant names:

• chr3-161788092-T-G
• rs10936243

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 0.444 in 151,870 control chromosomes in the GnomAD database, including 15,638 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 0.44 (15638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.444 AC: 67357 AN: 151752 Hom.: 15620 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.444 AC: 67403 AN: 151870 Hom.: 15638 Cov.: 32 AF XY: 0.450 AC XY: 33375 AN XY: 74208

African (AFR) AF: 0.367 AC: 15217 AN: 41430

American (AMR) AF: 0.495 AC: 7541 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4368 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1960 AN: 4806

European-Finnish (FIN) AF: 0.522 AC: 5497 AN: 10540

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30025 AN: 67908

Other (OTH) AF: 0.436 AC: 919 AN: 2110

Alfa AF: 0.327 Hom.: 1142

Bravo AF: 0.447

Asia WGS AF: 0.633 AC: 2194 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10936243; hg19: chr3-161505880;