1-91123257-A-G

Variant names:

• chr1-91123257-A-G
• rs346981

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 0.414 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

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 = 0.468 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: 0.414 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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.407

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346981; hg19: chr1-91588814;