chr10-112949509-C-T

Variant names:

• chr10-112949509-C-T
• rs10885395

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 0.201 in 151,974 control chromosomes in the GnomAD database, including 3,795 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 (3795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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: 0.201 AC: 30491 AN: 151860 Hom.: 3789 Cov.: 31

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.201 AC: 30502 AN: 151974 Hom.: 3795 Cov.: 31 AF XY: 0.199 AC XY: 14743 AN XY: 74260

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.222

Alfa AF: 0.236 Hom.: 790

Bravo AF: 0.194

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	9.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885395; hg19: chr10-114709268;