chr5-25494896-G-A

Variant names:

• chr5-25494896-G-A
• rs10078091

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 0.337 in 151,716 control chromosomes in the GnomAD database, including 8,988 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 0.34 (8988 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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: 0.337 AC: 51030 AN: 151598 Hom.: 8980 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.337 AC: 51068 AN: 151716 Hom.: 8988 Cov.: 31 AF XY: 0.338 AC XY: 25083 AN XY: 74116

African (AFR) AF: 0.445 AC: 18406 AN: 41364

American (AMR) AF: 0.355 AC: 5404 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3466

East Asian (EAS) AF: 0.159 AC: 821 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2863 AN: 10470

Middle Eastern (MID) AF: 0.323 AC: 93 AN: 288

European-Non Finnish (NFE) AF: 0.288 AC: 19566 AN: 67906

Other (OTH) AF: 0.303 AC: 638 AN: 2106

Alfa AF: 0.299 Hom.: 21324

Bravo AF: 0.338

Asia WGS AF: 0.305 AC: 1060 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.28
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10078091; hg19: chr5-25495005;