chr6-28326431-CCT-C

Position:

• chr6-28326431-CCT-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_030899.5(ZSCAN31):​c.954_955del​(p.Glu320LysfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00624 in 1,614,122 control chromosomes in the GnomAD database, including 42 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0055 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (39 hom.)
• Consequence: ZSCAN31 NM_030899.5 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.428

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 6-28326431-CCT-C is Benign according to our data. Variant chr6-28326431-CCT-C is described in ClinVar as [Benign]. Clinvar id is 787664.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN31	NM_030899.5	c.954_955del	p.Glu320LysfsTer4	frameshift_variant	4/4	ENST00000344279.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN31	ENST00000344279.11	c.954_955del	p.Glu320LysfsTer4	frameshift_variant	4/4	1	NM_030899.5	P1

Frequencies

GnomAD3 genomes AF: 0.00548 AC: 833 AN: 152114 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000845

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.00786

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.00924

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00637

Gnomad OTH AF: 0.00384

GnomAD3 exomes AF: 0.00631 AC: 1586 AN: 251420 Hom.: 10 AF XY: 0.00611 AC XY: 830 AN XY: 135876

Gnomad AFR exome AF: 0.000984

Gnomad AMR exome AF: 0.0109

Gnomad ASJ exome AF: 0.000595

Gnomad EAS exome AF: 0.00261

Gnomad SAS exome AF: 0.00513

Gnomad FIN exome AF: 0.0103

Gnomad NFE exome AF: 0.00642

Gnomad OTH exome AF: 0.00472

GnomAD4 exome AF: 0.00632 AC: 9233 AN: 1461890 Hom.: 39 AF XY: 0.00629 AC XY: 4574 AN XY: 727248

Gnomad4 AFR exome AF: 0.000926

Gnomad4 AMR exome AF: 0.0104

Gnomad4 ASJ exome AF: 0.000803

Gnomad4 EAS exome AF: 0.00766

Gnomad4 SAS exome AF: 0.00483

Gnomad4 FIN exome AF: 0.00981

Gnomad4 NFE exome AF: 0.00642

Gnomad4 OTH exome AF: 0.00520

GnomAD4 genome AF: 0.00547 AC: 832 AN: 152232 Hom.: 3 Cov.: 32 AF XY: 0.00555 AC XY: 413 AN XY: 74436

Gnomad4 AFR AF: 0.000843

Gnomad4 AMR AF: 0.00785

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.00924

Gnomad4 NFE AF: 0.00635

Gnomad4 OTH AF: 0.00380

Alfa AF: 0.00498 Hom.: 1

Bravo AF: 0.00547

Asia WGS AF: 0.00577 AC: 20 AN: 3478

EpiCase AF: 0.00540

EpiControl AF: 0.00605

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 28, 2017

- -

Computational scores

Source: dbNSFP v4.3

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: rs145866852; hg19: chr6-28294208;