chr2-116539957-T-A

Variant names:

• chr2-116539957-T-A
• rs2421608

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 0.299 in 152,050 control chromosomes in the GnomAD database, including 8,453 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 0.30 (8453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62
• 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 (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.299 AC: 45408 AN: 151932 Hom.: 8453 Cov.: 32

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.299 AC: 45422 AN: 152050 Hom.: 8453 Cov.: 32 AF XY: 0.303 AC XY: 22505 AN XY: 74300

African (AFR) AF: 0.0780 AC: 3239 AN: 41526

American (AMR) AF: 0.320 AC: 4885 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.577 AC: 2974 AN: 5154

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4820

European-Finnish (FIN) AF: 0.478 AC: 5045 AN: 10550

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25418 AN: 67966

Other (OTH) AF: 0.331 AC: 701 AN: 2116

Alfa AF: 0.336 Hom.: 1238

Bravo AF: 0.278

Asia WGS AF: 0.354 AC: 1231 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	0.022
DANN	Benign	0.15
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs2421608; hg19: chr2-117297533; COSMIC: COSV60098913;