1-80106373-A-G

Position:

• chr1-80106373-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 0.132 in 151,890 control chromosomes in the GnomAD database, including 1,913 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 0.13 (1913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20040 AN: 151774 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0880

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.132 AC: 20089 AN: 151890 Hom.: 1913 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74250

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.0880

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0752 Hom.: 468

Bravo AF: 0.139

Asia WGS AF: 0.242 AC: 833 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11162922; hg19: chr1-80572058; COSMIC: COSV59961964;