chr1-152640434-T-C

Position:

• chr1-152640434-T-C

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 0.193 in 152,162 control chromosomes in the GnomAD database, including 4,269 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 0.19 (4269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29365 AN: 152044 Hom.: 4247 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.193 AC: 29422 AN: 152162 Hom.: 4269 Cov.: 32 AF XY: 0.196 AC XY: 14571 AN XY: 74390

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.185

Alfa AF: 0.0963 Hom.: 1946

Bravo AF: 0.202

Asia WGS AF: 0.257 AC: 894 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	5.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325508; hg19: chr1-152612910;