rs11556953

Variant names:

• chr1-159918579-T-A
• rs11556953
• NM_003564.3:c.*221A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-159918579-T-A
• chr1-159918579-T-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001277224.2(TAGLN2):​c.*221A>T 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: 33)
• Consequence: TAGLN2 NM_001277224.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 2 publications found

Genes affected

TAGLN2 (HGNC:11554): (transgelin 2) The protein encoded by this gene is similar to the protein transgelin, which is one of the earliest markers of differentiated smooth muscle. The specific function of this protein has not yet been determined, although it is thought to be a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2013]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277224.2. 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
	TAGLN2	NM_003564.3	MANE Select	c.*221A>T		3_prime_UTR	Exon 5 of 5	NP_003555.1
	TAGLN2	NM_001277224.2		c.*221A>T		3_prime_UTR	Exon 5 of 5	NP_001264153.1
	TAGLN2	NM_001277223.2		c.*221A>T		3_prime_UTR	Exon 5 of 5	NP_001264152.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGLN2	ENST00000368097.9	TSL:1 MANE Select	c.*221A>T		3_prime_UTR	Exon 5 of 5	ENSP00000357077.5
	TAGLN2	ENST00000368096.5	TSL:1	c.*221A>T		3_prime_UTR	Exon 5 of 5	ENSP00000357076.1
	TAGLN2	ENST00000854583.1		c.*221A>T		3_prime_UTR	Exon 5 of 5	ENSP00000524642.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 6

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	6.6
DANN	Benign	0.84
PhyloP100		-0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11556953; hg19: chr1-159888369;