rs7537752

Variant names:

• chr1-109931820-C-G
• rs7537752

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 0.331 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.539 AC: 22342 AN: 41450

American (AMR) AF: 0.303 AC: 4633 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3373 AN: 5176

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3101 AN: 10570

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14090 AN: 67982

Other (OTH) AF: 0.288 AC: 606 AN: 2104

Alfa AF: 0.278 Hom.: 876

Bravo AF: 0.342

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.26
DANN	Benign	0.38
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7537752; hg19: chr1-110474442;