8-5633606-T-C

Variant names:

• chr8-5633606-T-C
• rs2733081

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 0.76 in 151,990 control chromosomes in the GnomAD database, including 44,228 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 0.76 (44228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.760 AC: 115469 AN: 151872 Hom.: 44222 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.760 AC: 115528 AN: 151990 Hom.: 44228 Cov.: 32 AF XY: 0.763 AC XY: 56659 AN XY: 74304

African (AFR) AF: 0.649 AC: 26894 AN: 41450

American (AMR) AF: 0.755 AC: 11527 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3849 AN: 5128

South Asian (SAS) AF: 0.787 AC: 3782 AN: 4806

European-Finnish (FIN) AF: 0.842 AC: 8923 AN: 10594

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54967 AN: 67956

Other (OTH) AF: 0.742 AC: 1567 AN: 2112

Alfa AF: 0.794 Hom.: 202874

Bravo AF: 0.747

Asia WGS AF: 0.727 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs2733081; hg19: chr8-5491128;