rs10886848

Positions:

• chr10-121081757-C-A
• chr10-121081757-C-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 0.357 in 152,006 control chromosomes in the GnomAD database, including 12,185 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 0.36 (12185 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54180 AN: 151888 Hom.: 12134 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.357 AC: 54292 AN: 152006 Hom.: 12185 Cov.: 33 AF XY: 0.364 AC XY: 27062 AN XY: 74304

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.336

Alfa AF: 0.233 Hom.: 2370

Bravo AF: 0.379

Asia WGS AF: 0.549 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886848; hg19: chr10-122841270;