2-29956980-T-A

Position:

• chr2-29956980-T-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 0.583 in 151,972 control chromosomes in the GnomAD database, including 26,283 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 0.58 (26283 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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: 0.583 AC: 88546 AN: 151852 Hom.: 26263 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.583 AC: 88603 AN: 151972 Hom.: 26283 Cov.: 31 AF XY: 0.580 AC XY: 43054 AN XY: 74260

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.582

Alfa AF: 0.612 Hom.: 3600

Bravo AF: 0.575

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11688196; hg19: chr2-30179846;