chr5-25658773-G-A

Variant names:

• chr5-25658773-G-A
• rs10076963

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.304 AC: 12581 AN: 41390

American (AMR) AF: 0.335 AC: 5101 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3464

East Asian (EAS) AF: 0.0984 AC: 507 AN: 5150

South Asian (SAS) AF: 0.294 AC: 1412 AN: 4810

European-Finnish (FIN) AF: 0.356 AC: 3738 AN: 10512

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20579 AN: 67942

Other (OTH) AF: 0.281 AC: 591 AN: 2104

Alfa AF: 0.296 Hom.: 25048

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
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs10076963; hg19: chr5-25658882;