rs10518115

chr4-73540998-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.2 in 152,160 control chromosomes in the GnomAD database, including 3,780 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 0.20 (3780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30367 AN: 152046 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.200 AC: 30384 AN: 152160 Hom.: 3780 Cov.: 32 AF XY: 0.202 AC XY: 15053 AN XY: 74368

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.246

Alfa AF: 0.215 Hom.: 466

Bravo AF: 0.202

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	7.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518115; hg19: chr4-74406715;