chr3-161786219-C-T

Variant names:

• chr3-161786219-C-T
• rs1996264

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.444 in 151,720 control chromosomes in the GnomAD database, including 15,648 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 (15648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.444 AC: 67343 AN: 151604 Hom.: 15630 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.444 AC: 67388 AN: 151720 Hom.: 15648 Cov.: 31 AF XY: 0.450 AC XY: 33401 AN XY: 74150

African (AFR) AF: 0.368 AC: 15169 AN: 41258

American (AMR) AF: 0.496 AC: 7555 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1552 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4356 AN: 5156

South Asian (SAS) AF: 0.408 AC: 1959 AN: 4804

European-Finnish (FIN) AF: 0.524 AC: 5535 AN: 10558

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

European-Non Finnish (NFE) AF: 0.442 AC: 30028 AN: 67928

Other (OTH) AF: 0.434 AC: 913 AN: 2104

Alfa AF: 0.448 Hom.: 60553

Bravo AF: 0.447

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1996264; hg19: chr3-161504007;