chr6-28329086-C-T

Variant names:

• chr6-28329086-C-T
• rs853679
• NM_030899.5:c.381+217G>A

Variant summary

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

The NM_030899.5(ZSCAN31):​c.381+217G>A 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: ZSCAN31 NM_030899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 29 publications found

Genes affected

ZSCAN31 (HGNC:14097): (zinc finger and SCAN domain containing 31) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ENSG00000294464 (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=-0.77).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030899.5. 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
	ZSCAN31	NM_030899.5	MANE Select	c.381+217G>A		intron	N/A	NP_112161.3
	ZSCAN31	NM_001135215.1		c.381+217G>A		intron	N/A	NP_001128687.1	Q96LW9-1
	ZSCAN31	NM_001135216.1		c.381+217G>A		intron	N/A	NP_001128688.1	Q96QL1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN31	ENST00000344279.11	TSL:1 MANE Select	c.381+217G>A		intron	N/A	ENSP00000345339.6	Q96LW9-1
	ZSCAN31	ENST00000396838.6	TSL:1	c.381+217G>A		intron	N/A	ENSP00000380050.2	Q96LW9-1
	ZSCAN31	ENST00000439158.5	TSL:1	c.381+217G>A		intron	N/A	ENSP00000413705.1	Q96LW9-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.8
DANN	Benign	0.79
PhyloP100		0.50

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: rs853679; hg19: chr6-28296863;