rs10484542

chr6-28341976-G-A

Variant summary

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

The ENST00000396838.6(ZSCAN31):c.-370-184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,126 control chromosomes in the GnomAD database, including 1,112 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 0.099 (1112 hom., cov: 32)
• Consequence: ZSCAN31 ENST00000396838.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN31	NM_001135215.1	c.-235-181C>T		intron_variant
ZSCAN31	NM_145909.3	c.-370-184C>T		intron_variant
ZSCAN31	XM_005249295.2	c.-249-5033C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN31	ENST00000396838.6	c.-370-184C>T		intron_variant		1		P1
ZSCAN31	ENST00000414429.5	c.-235-181C>T		intron_variant		2		P1
ZSCAN31	ENST00000426434.1	c.33+11886C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0993 AC: 15102 AN: 152010 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0994 AC: 15126 AN: 152126 Hom.: 1112 Cov.: 32 AF XY: 0.101 AC XY: 7498 AN XY: 74360

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0543 Hom.: 279

Bravo AF: 0.109

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.62
Dann	Benign	0.41

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: rs10484542; hg19: chr6-28309753;