rs853679

Variant names:

• chr6-28329086-C-A
• rs853679
• NM_030899.5:c.381+217G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-28329086-C-A
• chr6-28329086-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030899.5(ZSCAN31):​c.381+217G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,140 control chromosomes in the GnomAD database, including 3,629 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 0.19 (3629 hom., cov: 32)
• Consequence: ZSCAN31 NM_030899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 29 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]

ENSG00000294464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN31	NM_030899.5	c.381+217G>T		intron_variant	Intron 2 of 3	ENST00000344279.11	NP_112161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN31	ENST00000344279.11	c.381+217G>T		intron_variant	Intron 2 of 3	1	NM_030899.5	ENSP00000345339.6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29205 AN: 152024 Hom.: 3620 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.192 AC: 29230 AN: 152140 Hom.: 3629 Cov.: 32 AF XY: 0.184 AC XY: 13709 AN XY: 74408

African (AFR) AF: 0.347 AC: 14416 AN: 41486

American (AMR) AF: 0.164 AC: 2513 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3468

East Asian (EAS) AF: 0.126 AC: 655 AN: 5178

South Asian (SAS) AF: 0.0930 AC: 448 AN: 4818

European-Finnish (FIN) AF: 0.0562 AC: 596 AN: 10604

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.142 AC: 9632 AN: 67994

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.149 Hom.: 3528

Bravo AF: 0.211

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.83
PhyloP100		0.50
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: rs853679; hg19: chr6-28296863;