rs2796304

Variant names:

• chr10-29277054-C-A
• rs2796304

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;