2-68971256-T-C

Variant names:

• chr2-68971256-T-C
• rs4254535

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 0.305 in 152,084 control chromosomes in the GnomAD database, including 7,247 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 (7247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.305 AC: 46280 AN: 151966 Hom.: 7235 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.305 AC: 46326 AN: 152084 Hom.: 7247 Cov.: 32 AF XY: 0.300 AC XY: 22282 AN XY: 74340

African (AFR) AF: 0.384 AC: 15918 AN: 41496

American (AMR) AF: 0.252 AC: 3853 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 952 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5164

South Asian (SAS) AF: 0.189 AC: 913 AN: 4828

European-Finnish (FIN) AF: 0.276 AC: 2924 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19548 AN: 67956

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.292 Hom.: 30737

Bravo AF: 0.306

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.85
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs4254535; hg19: chr2-69198388; COSMIC: COSV65006148;