ENST00000562153.6:n.284+5470C>G

Variant names:

• chr16-72085224-G-C
• NM_017853.3:c.*1413C>G

Variant summary

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

The ENST00000562153.6(ENSG00000310525):​n.284+3763C>G variant causes a intron 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: 32)
• Consequence: ENSG00000310525 ENST00000562153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 0 publications found

Genes affected

TXNL4B (HGNC:26041): (thioredoxin like 4B) Predicted to be involved in mRNA splicing, via spliceosome. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000310525 (HGNC:):

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=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562153.6. 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
	TXNL4B	NM_017853.3	MANE Select	c.*1413C>G		3_prime_UTR	Exon 4 of 4	NP_060323.1	Q9NX01
	TXNL4B	NM_001142317.2		c.*1413C>G		3_prime_UTR	Exon 4 of 4	NP_001135789.1	Q9NX01
	TXNL4B	NM_001142318.2		c.*1413C>G		3_prime_UTR	Exon 4 of 4	NP_001135790.1	Q9NX01

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNL4B	ENST00000268483.8	TSL:1 MANE Select	c.*1413C>G		3_prime_UTR	Exon 4 of 4	ENSP00000268483.3	Q9NX01
	ENSG00000310525	ENST00000562153.6	TSL:4	n.284+3763C>G		intron	N/A	ENSP00000454635.2	H3BN11
	TXNL4B	ENST00000423037.5	TSL:4	c.*1413C>G		3_prime_UTR	Exon 4 of 4	ENSP00000408130.1	Q9NX01

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.39
PhyloP100		-0.66

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

hg19: chr16-72119123;