rs10511304

chr3-112075110-G-Achr3-112075110-G-T

Variant summary

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

The NM_001395507.1(TMPRSS7):c.1784-211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,160 control chromosomes in the GnomAD database, including 1,768 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 0.14 (1768 hom., cov: 33)
• Consequence: TMPRSS7 NM_001395507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMPRSS7	NM_001395507.1	c.1784-211G>A		intron_variant		ENST00000452346.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMPRSS7	ENST00000452346.7	c.1784-211G>A		intron_variant		5	NM_001395507.1
TMPRSS7	ENST00000419127.5	c.1406-211G>A		intron_variant		1		P1
TMPRSS7	ENST00000617607.4	c.1406-211G>A		intron_variant		5		P1
TMPRSS7	ENST00000435737.5	c.*1129-211G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20645 AN: 152042 Hom.: 1769 Cov.: 33

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.136 AC: 20639 AN: 152160 Hom.: 1768 Cov.: 33 AF XY: 0.134 AC XY: 9974 AN XY: 74366

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.139

Alfa AF: 0.181 Hom.: 3585

Bravo AF: 0.127

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.62
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: rs10511304; hg19: chr3-111793957;