11-105994705-T-C

Position:

• chr11-105994705-T-C

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 0.281 in 152,212 control chromosomes in the GnomAD database, including 5,998 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 0.28 (5998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.281 AC: 42684 AN: 152096 Hom.: 5991 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.281 AC: 42723 AN: 152212 Hom.: 5998 Cov.: 33 AF XY: 0.282 AC XY: 20977 AN XY: 74408

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.252

Alfa AF: 0.293 Hom.: 763

Bravo AF: 0.273

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895889; hg19: chr11-105865432;