2-81171409-A-G

Variant names:

• chr2-81171409-A-G
• rs1457342

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 0.518 in 151,824 control chromosomes in the GnomAD database, including 21,240 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 0.52 (21240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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 = 0.679 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: 0.518 AC: 78547 AN: 151706 Hom.: 21231 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.518 AC: 78590 AN: 151824 Hom.: 21240 Cov.: 32 AF XY: 0.530 AC XY: 39306 AN XY: 74198

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.542

Alfa AF: 0.535 Hom.: 4177

Bravo AF: 0.496

Asia WGS AF: 0.683 AC: 2378 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	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457342; hg19: chr2-81398533;