rs979965735

Variant names:

• chr12-117046583-C-A
• rs979965735
• NM_017899.4:c.495G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-117046583-C-A
• chr12-117046583-C-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_017899.4(TESC):​c.495G>T​(p.Ala165Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A165A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TESC NM_017899.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24
• Publications: 0 publications found

Genes affected

TESC (HGNC:26065): (tescalcin) Enables calcium ion binding activity. Involved in several processes, including cellular response to retinoic acid; positive regulation of macromolecule metabolic process; and positive regulation of myeloid cell differentiation. Located in several cellular components, including cytosol; lamellipodium; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP7: Synonymous conserved (PhyloP=-4.24 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017899.4. 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
	TESC	NM_017899.4	MANE Select	c.495G>T	p.Ala165Ala	synonymous	Exon 6 of 8	NP_060369.3	Q96BS2-1
	TESC	NM_001168325.2		c.414G>T	p.Ala138Ala	synonymous	Exon 5 of 7	NP_001161797.1	Q96BS2-3
	TESC	NR_031766.3		n.634G>T		non_coding_transcript_exon	Exon 6 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESC	ENST00000335209.12	TSL:1 MANE Select	c.495G>T	p.Ala165Ala	synonymous	Exon 6 of 8	ENSP00000334785.7	Q96BS2-1
	TESC	ENST00000940881.1		c.495G>T	p.Ala165Ala	synonymous	Exon 6 of 8	ENSP00000610940.1
	TESC	ENST00000874651.1		c.495G>T	p.Ala165Ala	synonymous	Exon 6 of 7	ENSP00000544710.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	1.3
DANN	Benign	0.87
PhyloP100		-4.2
PromoterAI		0.0096	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs979965735; hg19: chr12-117484388;