rs2796304

Positions:

• chr10-29277054-C-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 0.517 in 151,986 control chromosomes in the GnomAD database, including 20,352 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 (20352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 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: 0.517 AC: 78463 AN: 151866 Hom.: 20330 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.517 AC: 78503 AN: 151986 Hom.: 20352 Cov.: 33 AF XY: 0.515 AC XY: 38229 AN XY: 74280

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.515

Alfa AF: 0.525 Hom.: 8845

Bravo AF: 0.508

Asia WGS AF: 0.432 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.15
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2796304; hg19: chr10-29565983;