chr5-76797549-T-C

Variant names:

• chr5-76797549-T-C
• rs458591

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 0.676 in 152,060 control chromosomes in the GnomAD database, including 35,923 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 0.68 (35923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102666 AN: 151940 Hom.: 35860 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.676 AC: 102792 AN: 152060 Hom.: 35923 Cov.: 32 AF XY: 0.678 AC XY: 50409 AN XY: 74322

African (AFR) AF: 0.837 AC: 34743 AN: 41502

American (AMR) AF: 0.665 AC: 10146 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2640 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2128 AN: 5152

South Asian (SAS) AF: 0.788 AC: 3798 AN: 4820

European-Finnish (FIN) AF: 0.609 AC: 6428 AN: 10550

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40697 AN: 67978

Other (OTH) AF: 0.645 AC: 1364 AN: 2116

Alfa AF: 0.630 Hom.: 15491

Bravo AF: 0.684

Asia WGS AF: 0.639 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.98
DANN	Benign	0.54
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs458591; hg19: chr5-76093374; COSMIC: COSV53479523;