rs11190302

Positions:

• chr10-99873158-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 0.372 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;