1-152578800-A-G

Variant names:

• chr1-152578800-A-G
• rs4112788

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 0.669 in 151,748 control chromosomes in the GnomAD database, including 34,233 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 0.67 (34233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 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: 0.669 AC: 101476 AN: 151630 Hom.: 34189 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.669 AC: 101567 AN: 151748 Hom.: 34233 Cov.: 31 AF XY: 0.671 AC XY: 49700 AN XY: 74106

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.635

Alfa AF: 0.641 Hom.: 46938

Bravo AF: 0.667

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4112788; hg19: chr1-152551276;