3-79961384-C-G

Variant names:

• chr3-79961384-C-G
• rs1905343

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 151,998 control chromosomes in the GnomAD database, including 44,622 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 (44622 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.774 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: 0.765 AC: 116261 AN: 151878 Hom.: 44586 Cov.: 33

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.766 AC: 116358 AN: 151998 Hom.: 44622 Cov.: 33 AF XY: 0.765 AC XY: 56794 AN XY: 74284

African (AFR) AF: 0.748 AC: 30999 AN: 41468

American (AMR) AF: 0.780 AC: 11896 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2621 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3231 AN: 5140

South Asian (SAS) AF: 0.781 AC: 3769 AN: 4826

European-Finnish (FIN) AF: 0.778 AC: 8239 AN: 10586

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 52985 AN: 67940

Other (OTH) AF: 0.767 AC: 1618 AN: 2110

Alfa AF: 0.776 Hom.: 5684

Bravo AF: 0.761

Asia WGS AF: 0.715 AC: 2483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1905343; hg19: chr3-80010534;