rs7537752

chr1-109931820-C-G

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 0.331 in 152,058 control chromosomes in the GnomAD database, including 10,100 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 0.33 (10100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.331 AC: 50271 AN: 151940 Hom.: 10083 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.331 AC: 50335 AN: 152058 Hom.: 10100 Cov.: 32 AF XY: 0.336 AC XY: 25003 AN XY: 74318

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.288

Alfa AF: 0.293 Hom.: 742

Bravo AF: 0.342

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.26
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7537752; hg19: chr1-110474442;