2-135880646-T-C

Variant names:

• chr2-135880646-T-C
• rs632632

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 0.499 in 152,084 control chromosomes in the GnomAD database, including 23,002 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 0.50 (23002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.498 AC: 75734 AN: 151966 Hom.: 22953 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.499 AC: 75841 AN: 152084 Hom.: 23002 Cov.: 32 AF XY: 0.507 AC XY: 37726 AN XY: 74344

African (AFR) AF: 0.781 AC: 32393 AN: 41470

American (AMR) AF: 0.607 AC: 9277 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2476 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3302 AN: 5176

South Asian (SAS) AF: 0.659 AC: 3176 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3206 AN: 10576

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20370 AN: 67976

Other (OTH) AF: 0.573 AC: 1208 AN: 2110

Alfa AF: 0.424 Hom.: 5187

Bravo AF: 0.531

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs632632; hg19: chr2-136638216;