11-107567725-T-C

Position:

• chr11-107567725-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 0.439 in 151,962 control chromosomes in the GnomAD database, including 15,143 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 0.44 (15143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.439 AC: 66615 AN: 151844 Hom.: 15119 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.439 AC: 66688 AN: 151962 Hom.: 15143 Cov.: 32 AF XY: 0.438 AC XY: 32537 AN XY: 74276

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.412

Alfa AF: 0.407 Hom.: 8803

Bravo AF: 0.446

Asia WGS AF: 0.444 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs669715; hg19: chr11-107438451;