2-96176055-T-C

Variant names:

• chr2-96176055-T-C
• rs11886999

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 0.21 in 152,198 control chromosomes in the GnomAD database, including 3,577 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 (3577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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: 0.210 AC: 31935 AN: 152080 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.210 AC: 31995 AN: 152198 Hom.: 3577 Cov.: 32 AF XY: 0.213 AC XY: 15829 AN XY: 74410

African (AFR) AF: 0.160 AC: 6657 AN: 41532

American (AMR) AF: 0.268 AC: 4099 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1757 AN: 5172

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1825 AN: 10598

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14547 AN: 68012

Other (OTH) AF: 0.253 AC: 533 AN: 2106

Alfa AF: 0.213 Hom.: 3687

Bravo AF: 0.213

Asia WGS AF: 0.296 AC: 1028 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs11886999; hg19: chr2-96841793;