rs11190302

Variant names:

• chr10-99873158-C-T
• rs11190302

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 0.372 in 151,766 control chromosomes in the GnomAD database, including 11,067 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 0.37 (11067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 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: 0.371 AC: 56329 AN: 151648 Hom.: 11059 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.372 AC: 56386 AN: 151766 Hom.: 11067 Cov.: 32 AF XY: 0.370 AC XY: 27432 AN XY: 74178

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.406

Alfa AF: 0.401 Hom.: 4261

Bravo AF: 0.371

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11190302; hg19: chr10-101632915;