chr3-112075110-G-A

Variant names:

• chr3-112075110-G-A
• rs10511304
• NM_001395507.1:c.1784-211G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395507.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMPRSS7	NM_001395507.1	MANE Select	c.1784-211G>A		intron	N/A	NP_001382436.1
	TMPRSS7	NM_001042575.2		c.1406-211G>A		intron	N/A	NP_001036040.2
	TMPRSS7	NM_001366279.2		c.1373-211G>A		intron	N/A	NP_001353208.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMPRSS7	ENST00000452346.7	TSL:5 MANE Select	c.1784-211G>A		intron	N/A	ENSP00000398236.2
	TMPRSS7	ENST00000419127.5	TSL:1	c.1406-211G>A		intron	N/A	ENSP00000411645.1
	TMPRSS7	ENST00000617607.4	TSL:5	c.1406-211G>A		intron	N/A	ENSP00000478830.1

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

African (AFR) AF: 0.0430 AC: 1786 AN: 41526

American (AMR) AF: 0.115 AC: 1753 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2300 AN: 10554

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13293 AN: 68004

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.173 Hom.: 4635

Bravo AF: 0.127

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.62
DANN	Benign	0.53
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10511304; hg19: chr3-111793957;