2-96111420-T-G

Variant names:

• chr2-96111420-T-G
• rs2312955

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 0.71 in 152,172 control chromosomes in the GnomAD database, including 39,184 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 0.71 (39184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

ACMG classification

Verdict is Benign. Variant got -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 = 0.831 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: 0.710 AC: 108000 AN: 152054 Hom.: 39160 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.710 AC: 108076 AN: 152172 Hom.: 39184 Cov.: 32 AF XY: 0.706 AC XY: 52539 AN XY: 74382

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.744

Alfa AF: 0.685 Hom.: 41226

Bravo AF: 0.717

Asia WGS AF: 0.721 AC: 2507 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	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2312955; hg19: chr2-96777168;