rs10038113

Variant names:

• chr5-25902233-T-C
• rs10038113

Your query was ambiguous. Multiple possible variants found:

• chr5-25902233-T-C
• chr5-25902233-T-G

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 0.453 in 151,516 control chromosomes in the GnomAD database, including 15,999 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 0.45 (15999 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.453 AC: 68601 AN: 151398 Hom.: 15986 Cov.: 30

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.453 AC: 68668 AN: 151516 Hom.: 15999 Cov.: 30 AF XY: 0.455 AC XY: 33639 AN XY: 73960

African (AFR) AF: 0.542 AC: 22380 AN: 41298

American (AMR) AF: 0.415 AC: 6308 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3027 AN: 5044

South Asian (SAS) AF: 0.480 AC: 2301 AN: 4792

European-Finnish (FIN) AF: 0.425 AC: 4457 AN: 10490

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.409 AC: 27782 AN: 67912

Other (OTH) AF: 0.420 AC: 883 AN: 2100

Alfa AF: 0.421 Hom.: 39729

Bravo AF: 0.453

Asia WGS AF: 0.547 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.58
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs10038113; hg19: chr5-25902342;