rs645040

Variant names:

• chr3-136207780-G-T
• rs645040

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.753

Alfa AF: 0.775 Hom.: 56277

Bravo AF: 0.757

Asia WGS AF: 0.817 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs645040; hg19: chr3-135926622;