1-152914398-G-C

Variant names:

• chr1-152914398-G-C
• rs34599045

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.00138

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0331 Hom.: 22

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34599045; hg19: chr1-152886874;