chr2-46691526-A-G

Variant names:

• chr2-46691526-A-G
• rs7596521

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 0.309 in 152,104 control chromosomes in the GnomAD database, including 7,673 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 0.31 (7673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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: 0.309 AC: 46975 AN: 151984 Hom.: 7664 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.309 AC: 47017 AN: 152104 Hom.: 7673 Cov.: 32 AF XY: 0.306 AC XY: 22742 AN XY: 74366

African (AFR) AF: 0.417 AC: 17304 AN: 41480

American (AMR) AF: 0.319 AC: 4868 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1019 AN: 5182

South Asian (SAS) AF: 0.336 AC: 1620 AN: 4828

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10576

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18098 AN: 67972

Other (OTH) AF: 0.311 AC: 656 AN: 2112

Alfa AF: 0.288 Hom.: 5149

Bravo AF: 0.324

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.49
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7596521; hg19: chr2-46918665;