10-121334387-C-T

Variant names:

• chr10-121334387-C-T
• rs11199914

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 0.399 in 151,948 control chromosomes in the GnomAD database, including 12,902 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 0.40 (12902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 66 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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: 0.399 AC: 60612 AN: 151830 Hom.: 12879 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.399 AC: 60688 AN: 151948 Hom.: 12902 Cov.: 32 AF XY: 0.402 AC XY: 29837 AN XY: 74252

African (AFR) AF: 0.531 AC: 21974 AN: 41410

American (AMR) AF: 0.425 AC: 6494 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5158

South Asian (SAS) AF: 0.294 AC: 1413 AN: 4810

European-Finnish (FIN) AF: 0.429 AC: 4521 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21373 AN: 67964

Other (OTH) AF: 0.374 AC: 787 AN: 2102

Alfa AF: 0.346 Hom.: 20494

Bravo AF: 0.411

Asia WGS AF: 0.354 AC: 1230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11199914; hg19: chr10-123093901;