8-5633606-T-C

Variant names:

• chr8-5633606-T-C
• rs2733081

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 0.76 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.742

Alfa AF: 0.803 Hom.: 100238

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2733081; hg19: chr8-5491128;