rs6558132

Variant names:

• chr8-29613431-T-C
• rs6558132

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 0.492 in 152,134 control chromosomes in the GnomAD database, including 19,508 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 0.49 (19508 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 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: 0.491 AC: 74710 AN: 152014 Hom.: 19471 Cov.: 34

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.492 AC: 74800 AN: 152134 Hom.: 19508 Cov.: 34 AF XY: 0.482 AC XY: 35837 AN XY: 74374

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.490

Alfa AF: 0.462 Hom.: 2127

Bravo AF: 0.508

Asia WGS AF: 0.309 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6558132; hg19: chr8-29470947;