chr1-79733880-G-A

Variant names:

• chr1-79733880-G-A
• rs6672282

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 0.889 in 152,164 control chromosomes in the GnomAD database, including 60,607 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 0.89 (60607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135109 AN: 152046 Hom.: 60568 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.889 AC: 135201 AN: 152164 Hom.: 60607 Cov.: 32 AF XY: 0.889 AC XY: 66115 AN XY: 74402

African (AFR) AF: 0.757 AC: 31385 AN: 41470

American (AMR) AF: 0.926 AC: 14143 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3257 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4976 AN: 5184

South Asian (SAS) AF: 0.863 AC: 4160 AN: 4818

European-Finnish (FIN) AF: 0.965 AC: 10238 AN: 10612

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64108 AN: 68012

Other (OTH) AF: 0.884 AC: 1865 AN: 2110

Alfa AF: 0.912 Hom.: 11075

Bravo AF: 0.881

Asia WGS AF: 0.889 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6672282; hg19: chr1-80199565;