11-113690759-AG-A

Position:

• chr11-113690759-AG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_030770.4(TMPRSS5):​c.1063+81delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 1,284,390 control chromosomes in the GnomAD database, including 4,702 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1347 hom., cov: 30)
  • Exomes 𝑓: 0.069 (3355 hom.)
• Consequence: TMPRSS5 NM_030770.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.105

Genes affected

TMPRSS5 (HGNC:14908): (transmembrane serine protease 5) This gene encodes a protein that belongs to the serine protease family. Serine proteases are known to be involved in many physiological and pathological processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

TMPRSS5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-113690759-AG-A is Benign according to our data. Variant chr11-113690759-AG-A is described in ClinVar as [Benign]. Clinvar id is 1220624.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMPRSS5	NM_030770.4	c.1063+81delC		intron_variant		ENST00000299882.11	NP_110397.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMPRSS5	ENST00000299882.11	c.1063+81delC		intron_variant		1	NM_030770.4	ENSP00000299882.5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16866 AN: 151978 Hom.: 1345 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.119

GnomAD4 exome AF: 0.0694 AC: 78584 AN: 1132294 Hom.: 3355 AF XY: 0.0684 AC XY: 38866 AN XY: 567992

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.0588

Gnomad4 ASJ exome AF: 0.0883

Gnomad4 EAS exome AF: 0.000117

Gnomad4 SAS exome AF: 0.0436

Gnomad4 FIN exome AF: 0.0349

Gnomad4 NFE exome AF: 0.0707

Gnomad4 OTH exome AF: 0.0755

GnomAD4 genome AF: 0.111 AC: 16892 AN: 152096 Hom.: 1347 Cov.: 30 AF XY: 0.107 AC XY: 7974 AN XY: 74358

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0417

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0984 Hom.: 109

Bravo AF: 0.121

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs45570834; hg19: chr11-113561481;