11-118808920-A-T

Position:

• chr11-118808920-A-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 0.362 in 151,968 control chromosomes in the GnomAD database, including 10,870 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 0.36 (10870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

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 (AMR) allele frequency at 95% confidence interval = 0.498 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: 0.362 AC: 54994 AN: 151852 Hom.: 10862 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.362 AC: 55037 AN: 151968 Hom.: 10870 Cov.: 31 AF XY: 0.361 AC XY: 26831 AN XY: 74250

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.391

Alfa AF: 0.282 Hom.: 881

Bravo AF: 0.369

Asia WGS AF: 0.291 AC: 1013 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
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: rs1784300; hg19: chr11-118679629;