rs10886048

Variant names:

• chr10-117179371-T-C
• rs10886048

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.361 in 152,176 control chromosomes in the GnomAD database, including 11,118 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 (11118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.361 AC: 54856 AN: 152058 Hom.: 11089 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.361 AC: 54934 AN: 152176 Hom.: 11118 Cov.: 33 AF XY: 0.367 AC XY: 27289 AN XY: 74400

African (AFR) AF: 0.483 AC: 20025 AN: 41500

American (AMR) AF: 0.389 AC: 5955 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4012 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1843 AN: 4830

European-Finnish (FIN) AF: 0.310 AC: 3287 AN: 10588

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18047 AN: 67998

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.294 Hom.: 12267

Bravo AF: 0.377

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10886048; hg19: chr10-118938882;