1-91579198-G-T

Variant names:

• chr1-91579198-G-T
• rs10782968

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 0.808 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.838 AC: 34845 AN: 41560

American (AMR) AF: 0.850 AC: 13012 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2766 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5184

South Asian (SAS) AF: 0.933 AC: 4508 AN: 4830

European-Finnish (FIN) AF: 0.678 AC: 7167 AN: 10578

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52849 AN: 68012

Other (OTH) AF: 0.801 AC: 1695 AN: 2116

Alfa AF: 0.796 Hom.: 6366

Bravo AF: 0.821

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10782968; hg19: chr1-92044755;