2-133677253-T-C

Variant names:

• chr2-133677253-T-C
• rs7567288

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 0.213 in 152,164 control chromosomes in the GnomAD database, including 3,733 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 0.21 (3733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.213 AC: 32409 AN: 152046 Hom.: 3729 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.213 AC: 32436 AN: 152164 Hom.: 3733 Cov.: 32 AF XY: 0.215 AC XY: 15982 AN XY: 74404

African (AFR) AF: 0.283 AC: 11744 AN: 41502

American (AMR) AF: 0.175 AC: 2679 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3470

East Asian (EAS) AF: 0.0948 AC: 491 AN: 5180

South Asian (SAS) AF: 0.179 AC: 863 AN: 4824

European-Finnish (FIN) AF: 0.287 AC: 3038 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12487 AN: 68000

Other (OTH) AF: 0.184 AC: 388 AN: 2114

Alfa AF: 0.187 Hom.: 11323

Bravo AF: 0.206

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7567288; hg19: chr2-134434824; COSMIC: COSV66932086;