chr3-170310812-A-C

Variant names:

• chr3-170310812-A-C
• rs4955720

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 0.668 in 151,376 control chromosomes in the GnomAD database, including 34,373 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 0.67 (34373 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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: 0.668 AC: 101026 AN: 151276 Hom.: 34323 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.668 AC: 101128 AN: 151376 Hom.: 34373 Cov.: 30 AF XY: 0.664 AC XY: 49091 AN XY: 73900

African (AFR) AF: 0.788 AC: 32528 AN: 41278

American (AMR) AF: 0.666 AC: 10140 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1832 AN: 3466

East Asian (EAS) AF: 0.647 AC: 3318 AN: 5132

South Asian (SAS) AF: 0.742 AC: 3563 AN: 4800

European-Finnish (FIN) AF: 0.513 AC: 5272 AN: 10268

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42343 AN: 67910

Other (OTH) AF: 0.671 AC: 1414 AN: 2106

Alfa AF: 0.630 Hom.: 24482

Bravo AF: 0.682

Asia WGS AF: 0.727 AC: 2530 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.56
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs4955720; hg19: chr3-170028600;