chr2-41609173-T-C

Variant names:

• chr2-41609173-T-C
• rs7597606

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 0.658 in 151,974 control chromosomes in the GnomAD database, including 33,829 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 0.66 (33829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.658 AC: 99903 AN: 151856 Hom.: 33805 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.658 AC: 99966 AN: 151974 Hom.: 33829 Cov.: 32 AF XY: 0.653 AC XY: 48518 AN XY: 74274

African (AFR) AF: 0.830 AC: 34440 AN: 41492

American (AMR) AF: 0.603 AC: 9195 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1872 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2769 AN: 5168

South Asian (SAS) AF: 0.576 AC: 2771 AN: 4812

European-Finnish (FIN) AF: 0.596 AC: 6288 AN: 10548

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40664 AN: 67922

Other (OTH) AF: 0.621 AC: 1312 AN: 2114

Alfa AF: 0.614 Hom.: 110832

Bravo AF: 0.666

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.98
DANN	Benign	0.63
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7597606; hg19: chr2-41836313;