NM_024562.2:c.3108+16894C>G

Variant names:

• chr16-69057315-C-G
• rs11075704
• NM_024562.2:c.3108+16894C>G

Variant summary

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

The NM_024562.2(TANGO6):​c.3108+16894C>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: 31)
• Consequence: TANGO6 NM_024562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 10 publications found

Genes affected

TANGO6 (HGNC:25749): (transport and golgi organization 6 homolog) Predicted to be involved in protein secretion. Predicted to be integral component of membrane. [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=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANGO6	NM_024562.2	c.3108+16894C>G		intron_variant	Intron 17 of 17	ENST00000261778.2	NP_078838.1
TANGO6	XM_047434633.1	c.1695+16894C>G		intron_variant	Intron 11 of 11		XP_047290589.1
TANGO6	XM_047434634.1	c.1695+16894C>G		intron_variant	Intron 11 of 11		XP_047290590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANGO6	ENST00000261778.2	c.3108+16894C>G		intron_variant	Intron 17 of 17	1	NM_024562.2	ENSP00000261778.1
TANGO6	ENST00000561931.1	n.223+16894C>G		intron_variant	Intron 2 of 2	3
TANGO6	ENST00000562000.5	n.511+16894C>G		intron_variant	Intron 4 of 4	4
TANGO6	ENST00000568361.5	n.563+16894C>G		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.34

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: rs11075704; hg19: chr16-69091218;