rs53125

Variant names:

• chr7-128149144-G-C
• rs53125

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 0.409 in 152,052 control chromosomes in the GnomAD database, including 14,884 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 0.41 (14884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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: 0.409 AC: 62122 AN: 151934 Hom.: 14845 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.409 AC: 62220 AN: 152052 Hom.: 14884 Cov.: 32 AF XY: 0.413 AC XY: 30671 AN XY: 74330

African (AFR) AF: 0.652 AC: 27045 AN: 41482

American (AMR) AF: 0.459 AC: 7011 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2082 AN: 5154

South Asian (SAS) AF: 0.505 AC: 2437 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3387 AN: 10574

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18348 AN: 67956

Other (OTH) AF: 0.374 AC: 789 AN: 2108

Alfa AF: 0.340 Hom.: 1309

Bravo AF: 0.431

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs53125; hg19: chr7-127789196;