rs10928927

chr2-129710793-C-T

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 0.705 in 152,034 control chromosomes in the GnomAD database, including 40,587 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 (40587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 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: 0.706 AC: 107180 AN: 151916 Hom.: 40588 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.705 AC: 107205 AN: 152034 Hom.: 40587 Cov.: 32 AF XY: 0.707 AC XY: 52521 AN XY: 74298

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.740

Alfa AF: 0.828 Hom.: 57391

Bravo AF: 0.683

Asia WGS AF: 0.657 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.8
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10928927; hg19: chr2-130468366;