chr2-79130469-G-A

Variant names:

• chr2-79130469-G-A
• rs7603333

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 0.517 in 152,086 control chromosomes in the GnomAD database, including 20,822 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 0.52 (20822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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: 0.517 AC: 78597 AN: 151968 Hom.: 20812 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.517 AC: 78642 AN: 152086 Hom.: 20822 Cov.: 33 AF XY: 0.519 AC XY: 38594 AN XY: 74344

African (AFR) AF: 0.622 AC: 25792 AN: 41478

American (AMR) AF: 0.451 AC: 6899 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2624 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1992 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6604 AN: 10584

Middle Eastern (MID) AF: 0.362 AC: 105 AN: 290

European-Non Finnish (NFE) AF: 0.467 AC: 31760 AN: 67976

Other (OTH) AF: 0.449 AC: 949 AN: 2114

Alfa AF: 0.453 Hom.: 9061

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7603333; hg19: chr2-79357595;