chr2-72886395-G-A

Position:

• chr2-72886395-G-A

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 0.861 in 152,230 control chromosomes in the GnomAD database, including 57,068 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 0.86 (57068 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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 = 0.97 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: 0.861 AC: 131005 AN: 152112 Hom.: 57046 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.861 AC: 131070 AN: 152230 Hom.: 57068 Cov.: 33 AF XY: 0.866 AC XY: 64430 AN XY: 74428

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.869

Alfa AF: 0.895 Hom.: 78491

Bravo AF: 0.849

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421095; hg19: chr2-73113524;