1-160466663-A-G

Variant names:

• chr1-160466663-A-G
• rs1249564

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 0.736 in 151,694 control chromosomes in the GnomAD database, including 41,159 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 0.74 (41159 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 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: 0.736 AC: 111487 AN: 151576 Hom.: 41115 Cov.: 28

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.736 AC: 111582 AN: 151694 Hom.: 41159 Cov.: 28 AF XY: 0.736 AC XY: 54527 AN XY: 74094

African (AFR) AF: 0.728 AC: 30040 AN: 41266

American (AMR) AF: 0.696 AC: 10608 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2743 AN: 3466

East Asian (EAS) AF: 0.720 AC: 3714 AN: 5156

South Asian (SAS) AF: 0.793 AC: 3803 AN: 4794

European-Finnish (FIN) AF: 0.748 AC: 7870 AN: 10516

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50235 AN: 67952

Other (OTH) AF: 0.760 AC: 1593 AN: 2096

Alfa AF: 0.729 Hom.: 4750

Bravo AF: 0.732

Asia WGS AF: 0.736 AC: 2561 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	0.96
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1249564; hg19: chr1-160436453;