1-91123257-A-G

Position:

• chr1-91123257-A-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.91123257A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;