rs2527083

chr8-5647545-C-Achr8-5647545-C-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 0.747 in 151,950 control chromosomes in the GnomAD database, including 42,606 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 0.75 (42606 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 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: 0.747 AC: 113444 AN: 151832 Hom.: 42559 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.747 AC: 113556 AN: 151950 Hom.: 42606 Cov.: 30 AF XY: 0.747 AC XY: 55426 AN XY: 74236

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.750

Alfa AF: 0.756 Hom.: 59111

Bravo AF: 0.753

Asia WGS AF: 0.599 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.41
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2527083; hg19: chr8-5505067;