rs491546

chr8-92458612-G-T

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 0.0569 in 152,118 control chromosomes in the GnomAD database, including 325 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 0.057 (325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 8656 AN: 152000 Hom.: 323 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0569 AC: 8658 AN: 152118 Hom.: 325 Cov.: 31 AF XY: 0.0559 AC XY: 4161 AN XY: 74376

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0458 Hom.: 178

Bravo AF: 0.0593

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs491546; hg19: chr8-93470840;