2-24771701-T-C

Variant names:

• chr2-24771701-T-C
• rs9309308

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,746 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 0.18 (2746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.181 AC: 27572 AN: 152014 Hom.: 2745 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.181 AC: 27588 AN: 152132 Hom.: 2746 Cov.: 32 AF XY: 0.180 AC XY: 13418 AN XY: 74346

African (AFR) AF: 0.118 AC: 4882 AN: 41498

American (AMR) AF: 0.128 AC: 1951 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3466

East Asian (EAS) AF: 0.122 AC: 630 AN: 5172

South Asian (SAS) AF: 0.123 AC: 593 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2759 AN: 10576

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15222 AN: 67986

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.203 Hom.: 7638

Bravo AF: 0.170

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	7.2
DANN	Benign	0.81
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9309308; hg19: chr2-24994570;