chr3-112041632-A-G

Position:

• chr3-112041632-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395507.1(TMPRSS7):​c.299-288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,060 control chromosomes in the GnomAD database, including 36,316 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 0.65 (36316 hom., cov: 31)
• Consequence: TMPRSS7 NM_001395507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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]

TMPRSS7 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMPRSS7	NM_001395507.1	c.299-288A>G		intron_variant		ENST00000452346.7	NP_001382436.1
TMPRSS7	NM_001042575.2	c.-38-288A>G		intron_variant			NP_001036040.2
TMPRSS7	XM_011512754.2	c.50-288A>G		intron_variant			XP_011511056.1
TMPRSS7	NR_026734.1	n.133-288A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMPRSS7	ENST00000452346.7	c.299-288A>G		intron_variant		5	NM_001395507.1	ENSP00000398236.2
TMPRSS7	ENST00000419127.5	c.-38-288A>G		intron_variant		1		ENSP00000411645.1
TMPRSS7	ENST00000435737.5	n.-38-288A>G		intron_variant		2		ENSP00000415472.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98770 AN: 151940 Hom.: 36329 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.792

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.649 AC: 98756 AN: 152060 Hom.: 36316 Cov.: 31 AF XY: 0.651 AC XY: 48418 AN XY: 74356

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.687

Alfa AF: 0.756 Hom.: 36108

Bravo AF: 0.619

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.52

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: rs1844925; hg19: chr3-111760479;