1-76660688-C-A

Variant names:

• chr1-76660688-C-A
• rs551585

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 0.087 in 151,988 control chromosomes in the GnomAD database, including 777 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 0.087 (777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.166 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: 0.0869 AC: 13202 AN: 151872 Hom.: 775 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0591

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0870 AC: 13219 AN: 151988 Hom.: 777 Cov.: 32 AF XY: 0.0847 AC XY: 6297 AN XY: 74308

African (AFR) AF: 0.169 AC: 7016 AN: 41406

American (AMR) AF: 0.0581 AC: 887 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.0591 AC: 306 AN: 5180

South Asian (SAS) AF: 0.0526 AC: 253 AN: 4808

European-Finnish (FIN) AF: 0.0357 AC: 378 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3821 AN: 67956

Other (OTH) AF: 0.0811 AC: 171 AN: 2108

Alfa AF: 0.0655 Hom.: 567

Bravo AF: 0.0922

Asia WGS AF: 0.0540 AC: 188 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	0.76
DANN	Benign	0.76
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs551585; hg19: chr1-77126373;