chr5-34525826-A-G

Position:

• chr5-34525826-A-G

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 0.669 in 152,060 control chromosomes in the GnomAD database, including 34,910 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 0.67 (34910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.669 AC: 101605 AN: 151942 Hom.: 34896 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.669 AC: 101663 AN: 152060 Hom.: 34910 Cov.: 32 AF XY: 0.667 AC XY: 49605 AN XY: 74316

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.729

Alfa AF: 0.714 Hom.: 55395

Bravo AF: 0.683

Asia WGS AF: 0.878 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10075914; hg19: chr5-34525931;