chr1-159752266-C-T

Position:

• chr1-159752266-C-T

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 0.265 in 152,052 control chromosomes in the GnomAD database, including 6,741 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 0.26 (6741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.265 AC: 40229 AN: 151934 Hom.: 6738 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.265 AC: 40245 AN: 152052 Hom.: 6741 Cov.: 32 AF XY: 0.272 AC XY: 20178 AN XY: 74314

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.269

Alfa AF: 0.322 Hom.: 4281

Bravo AF: 0.249

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131568; hg19: chr1-159722056;