rs10505141

Variant names:

• chr8-110142557-T-C
• rs10505141

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 0.0838 in 152,118 control chromosomes in the GnomAD database, including 1,128 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 0.084 (1128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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: 0.0836 AC: 12705 AN: 152000 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.00914

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0643

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

GnomAD4 genome AF: 0.0838 AC: 12749 AN: 152118 Hom.: 1128 Cov.: 32 AF XY: 0.0834 AC XY: 6207 AN XY: 74382

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.0366

Gnomad4 FIN AF: 0.00914

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0516 Hom.: 80

Bravo AF: 0.0976

Asia WGS AF: 0.0890 AC: 306 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505141; hg19: chr8-111154786; COSMIC: COSV64832468;