1-91123257-A-G

Variant names:

• chr1-91123257-A-G
• rs346981

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 0.414 in 152,050 control chromosomes in the GnomAD database, including 13,317 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 0.41 (13317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.468 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62967 AN: 151934 Hom.: 13304 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.414 AC: 63005 AN: 152050 Hom.: 13317 Cov.: 33 AF XY: 0.417 AC XY: 30968 AN XY: 74318

African (AFR) AF: 0.474 AC: 19656 AN: 41482

American (AMR) AF: 0.393 AC: 6002 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2436 AN: 5156

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4754 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 25997 AN: 67960

Other (OTH) AF: 0.407 AC: 859 AN: 2110

Alfa AF: 0.394 Hom.: 5638

Bravo AF: 0.417

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs346981; hg19: chr1-91588814;