2-159913520-G-A

Position:

• chr2-159913520-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 0.714 in 152,096 control chromosomes in the GnomAD database, including 39,745 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 (39745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

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 = 0.793 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: 0.714 AC: 108489 AN: 151978 Hom.: 39711 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.714 AC: 108579 AN: 152096 Hom.: 39745 Cov.: 32 AF XY: 0.713 AC XY: 53043 AN XY: 74360

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.719

Alfa AF: 0.769 Hom.: 84233

Bravo AF: 0.709

Asia WGS AF: 0.708 AC: 2465 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	0.15
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12692575; hg19: chr2-160770031;