3-177992437-T-G

Variant names:

• chr3-177992437-T-G
• rs2160836

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 0.452 in 151,974 control chromosomes in the GnomAD database, including 20,354 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 0.45 (20354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.452 AC: 68622 AN: 151856 Hom.: 20284 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.452 AC: 68760 AN: 151974 Hom.: 20354 Cov.: 31 AF XY: 0.455 AC XY: 33811 AN XY: 74264

African (AFR) AF: 0.833 AC: 34520 AN: 41458

American (AMR) AF: 0.396 AC: 6041 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3470

East Asian (EAS) AF: 0.582 AC: 2992 AN: 5144

South Asian (SAS) AF: 0.519 AC: 2500 AN: 4820

European-Finnish (FIN) AF: 0.298 AC: 3148 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17235 AN: 67960

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.314 Hom.: 38970

Bravo AF: 0.474

Asia WGS AF: 0.603 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2160836; hg19: chr3-177710225;