ENST00000396838.6:c.-370-21A>G

Variant names:

• chr6-28341813-T-C
• rs6912584
• ENST00000396838.6:c.-370-21A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000396838.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN31	NM_001135215.1		c.-235-18A>G		intron	N/A	NP_001128687.1
	ZSCAN31	NM_145909.3		c.-370-21A>G		intron	N/A	NP_665916.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN31	ENST00000396838.6	TSL:1	c.-370-21A>G		intron	N/A	ENSP00000380050.2
	ZSCAN31	ENST00000414429.5	TSL:2	c.-235-18A>G		intron	N/A	ENSP00000390076.1
	ZSCAN31	ENST00000446222.5	TSL:3	c.-249-4870A>G		intron	N/A	ENSP00000411033.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.278 AC: 25 AN: 90

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.400 AC: 16563 AN: 41410

American (AMR) AF: 0.225 AC: 3435 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.102 AC: 528 AN: 5176

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4818

European-Finnish (FIN) AF: 0.113 AC: 1193 AN: 10602

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14249 AN: 67966

Other (OTH) AF: 0.262 AC: 552 AN: 2106

Alfa AF: 0.232 Hom.: 14474

Bravo AF: 0.270

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.21
PromoterAI		0.0036	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: rs6912584; hg19: chr6-28309590;