rs9525638

Variant names:

• chr13-42554441-T-C
• rs9525638

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 0.373 in 152,006 control chromosomes in the GnomAD database, including 11,386 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 0.37 (11386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.373 AC: 56699 AN: 151888 Hom.: 11389 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.373 AC: 56698 AN: 152006 Hom.: 11386 Cov.: 32 AF XY: 0.377 AC XY: 28018 AN XY: 74312

African (AFR) AF: 0.223 AC: 9239 AN: 41502

American (AMR) AF: 0.368 AC: 5624 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2261 AN: 5176

South Asian (SAS) AF: 0.354 AC: 1702 AN: 4812

European-Finnish (FIN) AF: 0.518 AC: 5463 AN: 10550

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29977 AN: 67912

Other (OTH) AF: 0.378 AC: 798 AN: 2110

Alfa AF: 0.415 Hom.: 36711

Bravo AF: 0.357

Asia WGS AF: 0.363 AC: 1260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.57
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs9525638; hg19: chr13-43128577;