rs853676

Variant names:

• chr6-28331910-C-T
• rs853676
• NM_030899.5:c.-95-2132G>A

Variant summary

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

The NM_030899.5(ZSCAN31):​c.-95-2132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,154 control chromosomes in the GnomAD database, including 3,320 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 (3320 hom., cov: 32)
• Consequence: ZSCAN31 NM_030899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN31	NM_030899.5	c.-95-2132G>A		intron_variant	Intron 1 of 3	ENST00000344279.11	NP_112161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN31	ENST00000344279.11	c.-95-2132G>A		intron_variant	Intron 1 of 3	1	NM_030899.5	ENSP00000345339.6

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28361 AN: 152036 Hom.: 3315 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.187 AC: 28383 AN: 152154 Hom.: 3320 Cov.: 32 AF XY: 0.179 AC XY: 13292 AN XY: 74406

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0931

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.175

Alfa AF: 0.146 Hom.: 2245

Bravo AF: 0.204

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	5.4
DANN	Benign	0.53

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: rs853676; hg19: chr6-28299687;