11-103718366-C-T

Position:

• chr11-103718366-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 0.45 in 151,992 control chromosomes in the GnomAD database, including 17,214 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 0.45 (17214 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103718366C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254987	ENST00000533459.1	n.128-13468G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68327 AN: 151874 Hom.: 17208 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.450 AC: 68348 AN: 151992 Hom.: 17214 Cov.: 32 AF XY: 0.455 AC XY: 33766 AN XY: 74282

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.456

Alfa AF: 0.497 Hom.: 3171

Bravo AF: 0.438

Asia WGS AF: 0.493 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917445; hg19: chr11-103589094;