rs11595716

chr10-112884177-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 0.337 in 151,944 control chromosomes in the GnomAD database, including 9,191 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 0.34 (9191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51160 AN: 151826 Hom.: 9167 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.337 AC: 51227 AN: 151944 Hom.: 9191 Cov.: 32 AF XY: 0.335 AC XY: 24858 AN XY: 74268

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.352

Alfa AF: 0.326 Hom.: 3942

Bravo AF: 0.335

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.5
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11595716; hg19: chr10-114643936;