6-28276799-C-T

Variant names:

• chr6-28276799-C-T
• NM_001023560.4:c.1143C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001023560.4(ZSCAN26):​c.1143C>T​(p.Leu381Leu) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZSCAN26 NM_001023560.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.78
• Publications: 0 publications found

Genes affected

ZSCAN26 (HGNC:12978): (zinc finger and SCAN domain containing 26) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000276302 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 6-28276799-C-T is Benign according to our data. Variant chr6-28276799-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3199410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.78 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001023560.4. 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
	ZSCAN26	NM_001023560.4	MANE Select	c.1143C>T	p.Leu381Leu	synonymous	Exon 4 of 4	NP_001018854.2	A0A024RCN4
	ZSCAN26	NM_001111039.3		c.1140C>T	p.Leu380Leu	synonymous	Exon 4 of 4	NP_001104509.1	Q16670-1
	ZSCAN26	NM_001287421.2		c.738C>T	p.Leu246Leu	synonymous	Exon 4 of 4	NP_001274350.1	A0A087X2F1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN26	ENST00000421553.7	TSL:1 MANE Select	c.1143C>T	p.Leu381Leu	synonymous	Exon 4 of 4	ENSP00000481707.1	A0A024RCN4
	ZSCAN26	ENST00000316606.10	TSL:1	c.738C>T	p.Leu246Leu	synonymous	Exon 4 of 4	ENSP00000484931.1	A0A087X2F1
	ENSG00000276302	ENST00000621053.1	TSL:4	c.133+4012C>T		intron	N/A	ENSP00000481142.1	A0A087WXM4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		-2.8

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: chr6-28244576;