NM_003564.3:c.*221A>G

Variant names:

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

Variant summary

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

The NM_003564.3(TAGLN2):​c.*221A>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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TAGLN2 NM_003564.3 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=-0.29).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAGLN2	NM_003564.3	c.*221A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000368097.9	NP_003555.1
TAGLN2	NM_001277224.2	c.*221A>G		3_prime_UTR_variant	Exon 5 of 5		NP_001264153.1
TAGLN2	NM_001277223.2	c.*221A>G		3_prime_UTR_variant	Exon 5 of 5		NP_001264152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAGLN2	ENST00000368097.9	c.*221A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_003564.3	ENSP00000357077.5
TAGLN2	ENST00000368096.5	c.*221A>G		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000357076.1
TAGLN2	ENST00000320307.8	c.*221A>G		downstream_gene_variant		3		ENSP00000357075.1
TAGLN2	ENST00000478033.1	n.*172A>G		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 420448 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 218920

African (AFR) AF: 0.00 AC: 0 AN: 11158

American (AMR) AF: 0.00 AC: 0 AN: 13708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11734

East Asian (EAS) AF: 0.00 AC: 0 AN: 26238

South Asian (SAS) AF: 0.00 AC: 0 AN: 32534

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25248

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1710

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 274766

Other (OTH) AF: 0.00 AC: 0 AN: 23352

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	8.0
DANN	Benign	0.76
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;