rs10076963

Variant names:

• chr5-25658773-G-A
• rs10076963

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 0.302 in 151,820 control chromosomes in the GnomAD database, including 7,106 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 0.30 (7106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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 (AMR) allele frequency at 95% confidence interval = 0.327 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: 0.302 AC: 45807 AN: 151702 Hom.: 7092 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.302 AC: 45856 AN: 151820 Hom.: 7106 Cov.: 32 AF XY: 0.303 AC XY: 22443 AN XY: 74184

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0984

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.281

Alfa AF: 0.291 Hom.: 10399

Bravo AF: 0.300

Asia WGS AF: 0.180 AC: 623 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	1.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10076963; hg19: chr5-25658882;