chr3-172501054-A-T

Variant names:

• chr3-172501054-A-T
• rs6785617

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.035 (19 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0906 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0350 AC: 1816 AN: 51866 Hom.: 19 Cov.: 0

Gnomad AFR AF: 0.0951

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.0405

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.00528

Gnomad FIN AF: 0.00450

Gnomad MID AF: 0.0152

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0350 AC: 1819 AN: 51940 Hom.: 19 Cov.: 0 AF XY: 0.0314 AC XY: 816 AN XY: 25962

African (AFR) AF: 0.0950 AC: 1241 AN: 13066

American (AMR) AF: 0.0113 AC: 71 AN: 6286

Ashkenazi Jewish (ASJ) AF: 0.0405 AC: 36 AN: 888

East Asian (EAS) AF: 0.00234 AC: 9 AN: 3840

South Asian (SAS) AF: 0.00528 AC: 13 AN: 2462

European-Finnish (FIN) AF: 0.00450 AC: 16 AN: 3556

Middle Eastern (MID) AF: 0.0156 AC: 1 AN: 64

European-Non Finnish (NFE) AF: 0.0199 AC: 413 AN: 20786

Other (OTH) AF: 0.0304 AC: 19 AN: 626

Alfa AF: 0.282 Hom.: 257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.29
DANN	Benign	0.044
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs6785617; hg19: chr3-172218844;