chr1-152914398-G-C

Variant names:

• chr1-152914398-G-C
• rs34599045

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 0.117 in 150,382 control chromosomes in the GnomAD database, including 1,342 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 0.12 (1342 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17513 AN: 150266 Hom.: 1337 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.00138

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.141

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17539 AN: 150382 Hom.: 1342 Cov.: 30 AF XY: 0.112 AC XY: 8241 AN XY: 73298

African (AFR) AF: 0.216 AC: 8858 AN: 40990

American (AMR) AF: 0.0780 AC: 1169 AN: 14978

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3468

East Asian (EAS) AF: 0.00138 AC: 7 AN: 5066

South Asian (SAS) AF: 0.0432 AC: 207 AN: 4788

European-Finnish (FIN) AF: 0.0590 AC: 592 AN: 10032

Middle Eastern (MID) AF: 0.144 AC: 41 AN: 284

European-Non Finnish (NFE) AF: 0.0900 AC: 6105 AN: 67796

Other (OTH) AF: 0.106 AC: 219 AN: 2070

Alfa AF: 0.0331 Hom.: 22

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.82
DANN	Benign	0.71
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs34599045; hg19: chr1-152886874;