rs537732

Variant names:

• chr1-115455628-C-T
• rs537732

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.619 AC: 25684 AN: 41468

American (AMR) AF: 0.262 AC: 4010 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5178

South Asian (SAS) AF: 0.232 AC: 1121 AN: 4822

European-Finnish (FIN) AF: 0.327 AC: 3455 AN: 10578

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18147 AN: 67988

Other (OTH) AF: 0.335 AC: 708 AN: 2114

Alfa AF: 0.299 Hom.: 23338

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs537732; hg19: chr1-115998249;