rs6912584

chr6-28341813-T-C

Variant summary

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

The ENST00000396838.6(ZSCAN31):c.-370-21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,142 control chromosomes in the GnomAD database, including 5,724 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 0.26 (5719 hom., cov: 32)
  • Exomes 𝑓: 0.25 (5 hom.)
• Consequence: ZSCAN31 ENST00000396838.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN31	NM_001135215.1	c.-235-18A>G		intron_variant
ZSCAN31	NM_145909.3	c.-370-21A>G		intron_variant
ZSCAN31	XM_005249295.2	c.-249-4870A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN31	ENST00000396838.6	c.-370-21A>G		intron_variant		1		P1
ZSCAN31	ENST00000414429.5	c.-235-18A>G		intron_variant		2		P1
ZSCAN31	ENST00000426434.1	c.33+12049A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38899 AN: 151918 Hom.: 5703 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.264

GnomAD4 exome AF: 0.250 AC: 27 AN: 108 Hom.: 5 Cov.: 0 AF XY: 0.280 AC XY: 23 AN XY: 82

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.256 AC: 38948 AN: 152034 Hom.: 5719 Cov.: 32 AF XY: 0.249 AC XY: 18536 AN XY: 74352

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.262

Alfa AF: 0.221 Hom.: 7489

Bravo AF: 0.270

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.9
Dann	Benign	0.48

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: rs6912584; hg19: chr6-28309590;