11-68747771-C-T

Variant summary

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

The NM_004923.3(TESMIN):c.472-405G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,032 control chromosomes in the GnomAD database, including 29,639 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 0.61 (29639 hom., cov: 32)
• Consequence: TESMIN NM_004923.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

TESMIN (HGNC:7446): (testis expressed metallothionein like protein) Metallothionein proteins are highly conserved low-molecular-weight cysteine-rich proteins that are induced by and bind to heavy metal ions and have no enzymatic activity. They may play a central role in the regulation of cell growth and differentiation and are involved in spermatogenesis. This gene encodes a metallothionein-like protein which has been shown to be expressed differentially in mouse testis and ovary. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TESMIN	NM_004923.3	c.472-405G>A		intron_variant		ENST00000255087.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TESMIN	ENST00000255087.10	c.472-405G>A		intron_variant		1	NM_004923.3	P1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92906 AN: 151914 Hom.: 29635 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.611 AC: 92935 AN: 152032 Hom.: 29639 Cov.: 32 AF XY: 0.624 AC XY: 46362 AN XY: 74316

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.605

Alfa AF: 0.620 Hom.: 3606

Bravo AF: 0.585

Asia WGS AF: 0.707 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.23
Dann	Benign	0.16

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: rs10896364; hg19: chr11-68515239;