chr1-76755677-A-G

Variant names:

• chr1-76755677-A-G
• rs2221083

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 0.875 in 152,064 control chromosomes in the GnomAD database, including 58,854 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 0.87 (58854 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• 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 = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132913 AN: 151946 Hom.: 58824 Cov.: 30

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.875 AC: 132994 AN: 152064 Hom.: 58854 Cov.: 30 AF XY: 0.877 AC XY: 65204 AN XY: 74320

African (AFR) AF: 0.719 AC: 29774 AN: 41412

American (AMR) AF: 0.919 AC: 14047 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3151 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5163 AN: 5166

South Asian (SAS) AF: 0.908 AC: 4375 AN: 4820

European-Finnish (FIN) AF: 0.963 AC: 10205 AN: 10596

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63334 AN: 67998

Other (OTH) AF: 0.866 AC: 1825 AN: 2108

Alfa AF: 0.912 Hom.: 120528

Bravo AF: 0.866

Asia WGS AF: 0.952 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2221083; hg19: chr1-77221362;