1-159766965-A-G

Variant names:

• chr1-159766965-A-G
• rs4364879

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 0.16 in 152,244 control chromosomes in the GnomAD database, including 2,372 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 0.16 (2372 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.160 AC: 24408 AN: 152126 Hom.: 2369 Cov.: 33

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.160 AC: 24415 AN: 152244 Hom.: 2372 Cov.: 33 AF XY: 0.168 AC XY: 12521 AN XY: 74434

African (AFR) AF: 0.0702 AC: 2919 AN: 41552

American (AMR) AF: 0.228 AC: 3489 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.135 AC: 701 AN: 5174

South Asian (SAS) AF: 0.119 AC: 577 AN: 4832

European-Finnish (FIN) AF: 0.327 AC: 3468 AN: 10592

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12269 AN: 67998

Other (OTH) AF: 0.129 AC: 272 AN: 2114

Alfa AF: 0.166 Hom.: 3375

Bravo AF: 0.150

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.77
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4364879; hg19: chr1-159736755;