rs10505141

chr8-110142557-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;