rs537732

chr1-115455628-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 0.364 in 152,106 control chromosomes in the GnomAD database, including 12,029 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 0.36 (12029 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.363 AC: 55216 AN: 151988 Hom.: 11994 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.364 AC: 55303 AN: 152106 Hom.: 12029 Cov.: 33 AF XY: 0.362 AC XY: 26951 AN XY: 74360

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.335

Alfa AF: 0.276 Hom.: 7094

Bravo AF: 0.369

Asia WGS AF: 0.240 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
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: rs537732; hg19: chr1-115998249;