2-96176055-T-C

Variant names:

• chr2-96176055-T-C
• rs11886999

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.253

Alfa AF: 0.218 Hom.: 1522

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11886999; hg19: chr2-96841793;