6-28276780-C-A

Variant names:

• chr6-28276780-C-A
• rs1361968542
• NM_001023560.4:c.1124C>A

Variant summary

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

The NM_001023560.4(ZSCAN26):​c.1124C>A​(p.Thr375Asn) variant causes a missense 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. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZSCAN26 NM_001023560.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.552
• 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: 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 (MetaRNN=0.11324921).

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.1124C>A	p.Thr375Asn	missense	Exon 4 of 4	NP_001018854.2	A0A024RCN4
	ZSCAN26	NM_001111039.3		c.1121C>A	p.Thr374Asn	missense	Exon 4 of 4	NP_001104509.1	Q16670-1
	ZSCAN26	NM_001287421.2		c.719C>A	p.Thr240Asn	missense	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.1124C>A	p.Thr375Asn	missense	Exon 4 of 4	ENSP00000481707.1	A0A024RCN4
	ZSCAN26	ENST00000316606.10	TSL:1	c.719C>A	p.Thr240Asn	missense	Exon 4 of 4	ENSP00000484931.1	A0A087X2F1
	ENSG00000276302	ENST00000621053.1	TSL:4	c.133+3993C>A		intron	N/A	ENSP00000481142.1	A0A087WXM4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.091	D
BayesDel_noAF	Benign	-0.11
CADD	Benign	19
DANN	Benign	0.77
DEOGEN2	Benign	0.032	T
FATHMM_MKL	Benign	0.26	N
LIST_S2	Benign	0.095	T
MetaRNN	Benign	0.11	T
PhyloP100		0.55
PrimateAI	Benign	0.44	T
Sift4G	Uncertain	0.014	D
Polyphen		0.98	D
Vest4		0.26
MVP		0.26
GERP RS		3.2
Varity_R		0.074
gMVP		0.060

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: rs1361968542; hg19: chr6-28244557;