rs7603333

Variant names:

• chr2-79130469-G-A
• rs7603333

Your query was ambiguous. Multiple possible variants found:

• chr2-79130469-G-A
• chr2-79130469-G-T

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 0.517 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.449

Alfa AF: 0.451 Hom.: 8093

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7603333; hg19: chr2-79357595;