rs13225753

Variant names:

• chr7-82529207-A-G
• rs13225753

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 0.0559 in 152,282 control chromosomes in the GnomAD database, including 463 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 0.056 (463 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8504 AN: 152164 Hom.: 459 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0559 AC: 8515 AN: 152282 Hom.: 463 Cov.: 33 AF XY: 0.0597 AC XY: 4446 AN XY: 74450

African (AFR) AF: 0.0133 AC: 551 AN: 41582

American (AMR) AF: 0.121 AC: 1850 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1316 AN: 5150

South Asian (SAS) AF: 0.0757 AC: 365 AN: 4824

European-Finnish (FIN) AF: 0.0741 AC: 787 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3246 AN: 68026

Other (OTH) AF: 0.0578 AC: 122 AN: 2110

Alfa AF: 0.0499 Hom.: 120

Bravo AF: 0.0576

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs13225753; hg19: chr7-82158523;