1-151982533-C-T

Position:

• chr1-151982533-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 0.282 in 152,134 control chromosomes in the GnomAD database, including 6,481 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 0.28 (6481 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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: 0.282 AC: 42933 AN: 152014 Hom.: 6482 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.282 AC: 42944 AN: 152134 Hom.: 6481 Cov.: 33 AF XY: 0.284 AC XY: 21095 AN XY: 74362

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.284

Alfa AF: 0.276 Hom.: 1308

Bravo AF: 0.273

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6678672; hg19: chr1-151955009;