1-166809517-C-A

Variant names:

• chr1-166809517-C-A
• rs2205647

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 0.714 in 152,094 control chromosomes in the GnomAD database, including 39,140 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 0.71 (39140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.713 AC: 108418 AN: 151976 Hom.: 39084 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.714 AC: 108532 AN: 152094 Hom.: 39140 Cov.: 32 AF XY: 0.713 AC XY: 53030 AN XY: 74340

African (AFR) AF: 0.802 AC: 33279 AN: 41518

American (AMR) AF: 0.741 AC: 11306 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2407 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4457 AN: 5162

South Asian (SAS) AF: 0.737 AC: 3554 AN: 4822

European-Finnish (FIN) AF: 0.622 AC: 6573 AN: 10562

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44551 AN: 67980

Other (OTH) AF: 0.727 AC: 1534 AN: 2110

Alfa AF: 0.687 Hom.: 106543

Bravo AF: 0.730

Asia WGS AF: 0.768 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.44
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2205647; hg19: chr1-166778754;