3-112050311-T-C

Position:

• chr3-112050311-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001395507.1(TMPRSS7):​c.1090+337T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 152,014 control chromosomes in the GnomAD database, including 141 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 0.035 (141 hom., cov: 31)
• Consequence: TMPRSS7 NM_001395507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

TMPRSS7 (HGNC:30846): (transmembrane serine protease 7) Predicted to enable serine-type peptidase activity. Predicted to be involved in proteolysis. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0354 (5376/152014) while in subpopulation NFE AF= 0.0485 (3294/67942). AF 95% confidence interval is 0.0471. There are 141 homozygotes in gnomad4. There are 2653 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 141 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMPRSS7	NM_001395507.1	c.1090+337T>C		intron_variant		ENST00000452346.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMPRSS7	ENST00000452346.7	c.1090+337T>C		intron_variant		5	NM_001395507.1
TMPRSS7	ENST00000419127.5	c.712+337T>C		intron_variant		1		P1
TMPRSS7	ENST00000617607.4	c.712+337T>C		intron_variant		5		P1
TMPRSS7	ENST00000435737.5	c.*435+337T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5379 AN: 151896 Hom.: 141 Cov.: 31

Gnomad AFR AF: 0.00810

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0354 AC: 5376 AN: 152014 Hom.: 141 Cov.: 31 AF XY: 0.0357 AC XY: 2653 AN XY: 74298

Gnomad4 AFR AF: 0.00807

Gnomad4 AMR AF: 0.0297

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0380

Alfa AF: 0.0449 Hom.: 85

Bravo AF: 0.0315

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.53

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: rs2399403; hg19: chr3-111769158;