chr8-5647545-C-A

Variant names:

• chr8-5647545-C-A
• rs2527083

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 0.747 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.733 AC: 30374 AN: 41428

American (AMR) AF: 0.828 AC: 12641 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2848 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2896 AN: 5140

South Asian (SAS) AF: 0.674 AC: 3240 AN: 4810

European-Finnish (FIN) AF: 0.732 AC: 7738 AN: 10568

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51238 AN: 67946

Other (OTH) AF: 0.750 AC: 1583 AN: 2110

Alfa AF: 0.754 Hom.: 81625

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2527083; hg19: chr8-5505067;