3-112779033-T-C

Variant names:

• chr3-112779033-T-C
• rs1002979

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 0.558 in 152,050 control chromosomes in the GnomAD database, including 24,564 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 0.56 (24564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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: 0.558 AC: 84754 AN: 151932 Hom.: 24517 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.558 AC: 84855 AN: 152050 Hom.: 24564 Cov.: 33 AF XY: 0.560 AC XY: 41645 AN XY: 74312

African (AFR) AF: 0.715 AC: 29645 AN: 41462

American (AMR) AF: 0.534 AC: 8161 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3350 AN: 5176

South Asian (SAS) AF: 0.537 AC: 2592 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5684 AN: 10548

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32068 AN: 67986

Other (OTH) AF: 0.552 AC: 1163 AN: 2106

Alfa AF: 0.509 Hom.: 38103

Bravo AF: 0.566

Asia WGS AF: 0.622 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.84
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1002979; hg19: chr3-112497880;