rs10484542

Variant names:

• chr6-28341976-G-A
• rs10484542
• ENST00000396838.6:c.-370-184C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZSCAN31	NM_001135215.1	c.-235-181C>T		intron_variant	Intron 3 of 7		NP_001128687.1
ZSCAN31	NM_145909.3	c.-370-184C>T		intron_variant	Intron 2 of 7		NP_665916.1
ZSCAN31	XM_005249295.2	c.-249-5033C>T		intron_variant	Intron 1 of 4		XP_005249352.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN31	ENST00000396838.6	c.-370-184C>T		intron_variant	Intron 2 of 7	1		ENSP00000380050.2
ZSCAN31	ENST00000414429.5	c.-235-181C>T		intron_variant	Intron 3 of 7	2		ENSP00000390076.1
ZSCAN31	ENST00000446222.5	c.-249-5033C>T		intron_variant	Intron 2 of 3	3		ENSP00000411033.1

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

African (AFR) AF: 0.169 AC: 7002 AN: 41484

American (AMR) AF: 0.124 AC: 1895 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1605 AN: 5164

South Asian (SAS) AF: 0.126 AC: 608 AN: 4818

European-Finnish (FIN) AF: 0.0518 AC: 548 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0436 AC: 2966 AN: 67996

Other (OTH) AF: 0.0846 AC: 178 AN: 2104

Alfa AF: 0.0618 Hom.: 487

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
PhyloP100		-2.3
PromoterAI		0.0076	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs10484542; hg19: chr6-28309753;