6-28329086-C-A

Position:

• chr6-28329086-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030899.5(ZSCAN31):​c.381+217G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,140 control chromosomes in the GnomAD database, including 3,629 homozygotes. 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: 𝑓 0.19 (3629 hom., cov: 32)
• Consequence: ZSCAN31 NM_030899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

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]

ZSCAN31 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN31	NM_030899.5	c.381+217G>T		intron_variant		ENST00000344279.11	NP_112161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN31	ENST00000344279.11	c.381+217G>T		intron_variant		1	NM_030899.5	ENSP00000345339.6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29205 AN: 152024 Hom.: 3620 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.192 AC: 29230 AN: 152140 Hom.: 3629 Cov.: 32 AF XY: 0.184 AC XY: 13709 AN XY: 74408

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.177

Alfa AF: 0.138 Hom.: 2037

Bravo AF: 0.211

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs853679; hg19: chr6-28296863;