rs538776

Variant names:

• chr5-58887360-T-C
• rs538776

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 0.0977 in 152,230 control chromosomes in the GnomAD database, including 772 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 0.098 (772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• 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 (SAS) allele frequency at 95% confidence interval = 0.104 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: 0.0977 AC: 14866 AN: 152112 Hom.: 767 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0977 AC: 14879 AN: 152230 Hom.: 772 Cov.: 32 AF XY: 0.100 AC XY: 7469 AN XY: 74438

African (AFR) AF: 0.106 AC: 4413 AN: 41522

American (AMR) AF: 0.0920 AC: 1409 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3468

East Asian (EAS) AF: 0.0752 AC: 389 AN: 5174

South Asian (SAS) AF: 0.108 AC: 524 AN: 4830

European-Finnish (FIN) AF: 0.135 AC: 1426 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6198 AN: 68016

Other (OTH) AF: 0.0901 AC: 190 AN: 2108

Alfa AF: 0.0943 Hom.: 1293

Bravo AF: 0.0953

Asia WGS AF: 0.0900 AC: 315 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	0.33
DANN	Benign	0.61
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs538776; hg19: chr5-58183187;