1-91579198-G-T

Position:

• chr1-91579198-G-T

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 0.808 in 152,262 control chromosomes in the GnomAD database, including 50,008 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 0.81 (50008 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91579198G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122939 AN: 152144 Hom.: 49968 Cov.: 34

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.808 AC: 123036 AN: 152262 Hom.: 50008 Cov.: 34 AF XY: 0.808 AC XY: 60150 AN XY: 74438

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.801

Alfa AF: 0.795 Hom.: 6089

Bravo AF: 0.821

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10782968; hg19: chr1-92044755;