rs645040

Variant names:

• chr3-136207780-G-T
• rs645040

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 0.766 in 152,206 control chromosomes in the GnomAD database, including 44,836 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 0.77 (44836 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 95 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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: 0.766 AC: 116479 AN: 152088 Hom.: 44800 Cov.: 34

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.766 AC: 116572 AN: 152206 Hom.: 44836 Cov.: 34 AF XY: 0.768 AC XY: 57184 AN XY: 74412

African (AFR) AF: 0.707 AC: 29340 AN: 41516

American (AMR) AF: 0.778 AC: 11894 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2399 AN: 3468

East Asian (EAS) AF: 0.866 AC: 4496 AN: 5194

South Asian (SAS) AF: 0.755 AC: 3637 AN: 4820

European-Finnish (FIN) AF: 0.865 AC: 9172 AN: 10602

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53219 AN: 68004

Other (OTH) AF: 0.753 AC: 1590 AN: 2112

Alfa AF: 0.774 Hom.: 140870

Bravo AF: 0.757

Asia WGS AF: 0.817 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.9
DANN	Benign	0.58
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs645040; hg19: chr3-135926622;