11-68732406-C-T

Variant names:

• chr11-68732406-C-T
• rs4930243
• NM_004923.3:c.917+6294G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004923.3(TESMIN):​c.917+6294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,050 control chromosomes in the GnomAD database, including 20,693 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 0.51 (20693 hom., cov: 32)
• Consequence: TESMIN NM_004923.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004923.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESMIN	NM_004923.3	MANE Select	c.917+6294G>A		intron	N/A	NP_004914.2	Q9Y4I5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESMIN	ENST00000255087.10	TSL:1 MANE Select	c.917+6294G>A		intron	N/A	ENSP00000255087.5	Q9Y4I5-1
	TESMIN	ENST00000936460.1		c.917+6294G>A		intron	N/A	ENSP00000606519.1
	TESMIN	ENST00000865611.1		c.719+6294G>A		intron	N/A	ENSP00000535670.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76894 AN: 151930 Hom.: 20687 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.506 AC: 76913 AN: 152050 Hom.: 20693 Cov.: 32 AF XY: 0.521 AC XY: 38734 AN XY: 74324

African (AFR) AF: 0.350 AC: 14510 AN: 41458

American (AMR) AF: 0.555 AC: 8489 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1607 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3883 AN: 5172

South Asian (SAS) AF: 0.624 AC: 3009 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7879 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36130 AN: 67960

Other (OTH) AF: 0.482 AC: 1017 AN: 2110

Alfa AF: 0.529 Hom.: 18399

Bravo AF: 0.480

Asia WGS AF: 0.667 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		1.1
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: rs4930243; hg19: chr11-68499874;