1-152791480-A-G

Position:

• chr1-152791480-A-G

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 0.155 in 134,804 control chromosomes in the GnomAD database, including 5,756 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 0.15 (5756 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 20828 AN: 134702 Hom.: 5744 Cov.: 22

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0787

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0735

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.155 AC: 20867 AN: 134804 Hom.: 5756 Cov.: 22 AF XY: 0.152 AC XY: 10039 AN XY: 65844

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.0390

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.0537

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.123

Alfa AF: 0.137 Hom.: 453

Asia WGS AF: 0.0980 AC: 336 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12086263; hg19: chr1-152763956;