NM_001105556.3:c.*542C>G

Variant names:

• chr1-27886464-C-G
• rs6564
• NM_001105556.3:c.*542C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001105556.3(THEMIS2):​c.*542C>G variant causes a 3 prime UTR 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: THEMIS2 NM_001105556.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 0 publications found

Genes affected

THEMIS2 (HGNC:16839): (thymocyte selection associated family member 2) Predicted to be involved in T cell receptor signaling pathway and regulation of B cell activation. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105556.3. 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
	THEMIS2	NM_001105556.3	MANE Select	c.*542C>G		3_prime_UTR	Exon 6 of 6	NP_001099026.1	Q5TEJ8-1
	THEMIS2	NM_001286113.2		c.*542C>G		3_prime_UTR	Exon 7 of 7	NP_001273042.1	Q5TEJ8-5
	THEMIS2	NM_001286115.2		c.*542C>G		3_prime_UTR	Exon 6 of 6	NP_001273044.1	Q5TEJ8-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THEMIS2	ENST00000373921.8	TSL:5 MANE Select	c.*542C>G		3_prime_UTR	Exon 6 of 6	ENSP00000363031.3	Q5TEJ8-1
	THEMIS2	ENST00000456990.1	TSL:1	c.*542C>G		3_prime_UTR	Exon 5 of 5	ENSP00000398049.1	H7C124
	THEMIS2	ENST00000373925.5	TSL:1	c.*618C>G		3_prime_UTR	Exon 5 of 5	ENSP00000363035.1	Q5TEJ8-2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.67
DANN	Benign	0.46
PhyloP100		-0.46

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: rs6564; hg19: chr1-28212975;