2-96745212-A-G

Position:

• chr2-96745212-A-G

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 0.256 in 151,952 control chromosomes in the GnomAD database, including 5,985 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 0.26 (5985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38967 AN: 151834 Hom.: 5992 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.256 AC: 38962 AN: 151952 Hom.: 5985 Cov.: 31 AF XY: 0.260 AC XY: 19313 AN XY: 74234

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.207

Alfa AF: 0.297 Hom.: 12471

Bravo AF: 0.232

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6746896; hg19: chr2-97410949;