rs491546

Variant names:

• chr8-92458612-G-T
• rs491546

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 0.0569 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0997 AC: 4137 AN: 41474

American (AMR) AF: 0.0418 AC: 639 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3468

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5164

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4820

European-Finnish (FIN) AF: 0.0436 AC: 462 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0428 AC: 2907 AN: 67996

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0479 Hom.: 260

Bravo AF: 0.0593

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.49
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs491546; hg19: chr8-93470840;