2-129427605-A-G

Position:

• chr2-129427605-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 0.494 in 152,104 control chromosomes in the GnomAD database, including 22,541 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 0.49 (22541 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75174 AN: 151986 Hom.: 22544 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.494 AC: 75176 AN: 152104 Hom.: 22541 Cov.: 33 AF XY: 0.496 AC XY: 36889 AN XY: 74356

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.503

Alfa AF: 0.571 Hom.: 3406

Bravo AF: 0.468

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17049450; hg19: chr2-130185178;