11-72181445-T-C

Position:

• chr11-72181445-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 (7 hom., cov: 43)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72181445T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000204971	ENST00000378140.3	n.419+17068A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 54346 AN: 119570 Hom.: 4 Cov.: 43 FAILED QC

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.467

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.455 AC: 54392 AN: 119672 Hom.: 7 Cov.: 43 AF XY: 0.453 AC XY: 26533 AN XY: 58522

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.467

Alfa AF: 0.336 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3887687; hg19: chr11-71892489; COSMIC: COSV65379560;