2-240357619-C-T

Variant names:

• chr2-240357619-C-T
• rs7609518

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 0.785 in 148,312 control chromosomes in the GnomAD database, including 46,096 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 0.79 (46096 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.785 AC: 116337 AN: 148196 Hom.: 46053 Cov.: 23

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.727

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.785 AC: 116435 AN: 148312 Hom.: 46096 Cov.: 23 AF XY: 0.780 AC XY: 56186 AN XY: 72062

African (AFR) AF: 0.890 AC: 35971 AN: 40432

American (AMR) AF: 0.696 AC: 10154 AN: 14586

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2315 AN: 3434

East Asian (EAS) AF: 0.409 AC: 1925 AN: 4712

South Asian (SAS) AF: 0.677 AC: 3105 AN: 4588

European-Finnish (FIN) AF: 0.808 AC: 8016 AN: 9916

Middle Eastern (MID) AF: 0.731 AC: 209 AN: 286

European-Non Finnish (NFE) AF: 0.777 AC: 52386 AN: 67402

Other (OTH) AF: 0.743 AC: 1526 AN: 2054

Alfa AF: 0.762 Hom.: 52746

Bravo AF: 0.775

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.93
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7609518; hg19: chr2-241297036;