chr1-91104132-G-A

Variant names:

• chr1-91104132-G-A
• rs164898

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 0.755 in 152,182 control chromosomes in the GnomAD database, including 43,602 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 0.76 (43602 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114836 AN: 152064 Hom.: 43553 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.755 AC: 114941 AN: 152182 Hom.: 43602 Cov.: 33 AF XY: 0.761 AC XY: 56604 AN XY: 74370

African (AFR) AF: 0.825 AC: 34276 AN: 41524

American (AMR) AF: 0.723 AC: 11054 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2425 AN: 3472

East Asian (EAS) AF: 0.868 AC: 4500 AN: 5184

South Asian (SAS) AF: 0.732 AC: 3520 AN: 4812

European-Finnish (FIN) AF: 0.794 AC: 8405 AN: 10580

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48447 AN: 68010

Other (OTH) AF: 0.726 AC: 1535 AN: 2114

Alfa AF: 0.720 Hom.: 137034

Bravo AF: 0.751

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.013
DANN	Benign	0.65
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs164898; hg19: chr1-91569689;