1-80929175-A-G

Variant names:

• chr1-80929175-A-G
• rs6678267

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 0.796 in 150,698 control chromosomes in the GnomAD database, including 47,767 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 0.80 (47767 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.802 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: 0.796 AC: 119869 AN: 150592 Hom.: 47747 Cov.: 27

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.796 AC: 119933 AN: 150698 Hom.: 47767 Cov.: 27 AF XY: 0.800 AC XY: 58787 AN XY: 73528

African (AFR) AF: 0.789 AC: 32337 AN: 41010

American (AMR) AF: 0.814 AC: 12319 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2986 AN: 3458

East Asian (EAS) AF: 0.686 AC: 3513 AN: 5124

South Asian (SAS) AF: 0.791 AC: 3786 AN: 4784

European-Finnish (FIN) AF: 0.833 AC: 8497 AN: 10196

Middle Eastern (MID) AF: 0.862 AC: 250 AN: 290

European-Non Finnish (NFE) AF: 0.796 AC: 53883 AN: 67730

Other (OTH) AF: 0.826 AC: 1712 AN: 2072

Alfa AF: 0.802 Hom.: 5961

Bravo AF: 0.794

Asia WGS AF: 0.737 AC: 2558 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.20
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6678267; hg19: chr1-81394860;