rs202906

chr6-28043874-T-C

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):n.188+16504A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,068 control chromosomes in the GnomAD database, including 1,333 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 0.13 (1333 hom., cov: 29)
• Consequence: ZSCAN16-AS1 ENST00000660873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN16-AS1	ENST00000660873.1	n.188+16504A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19317 AN: 151956 Hom.: 1330 Cov.: 29

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.127 AC: 19343 AN: 152068 Hom.: 1333 Cov.: 29 AF XY: 0.123 AC XY: 9141 AN XY: 74336

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0935

Gnomad4 FIN AF: 0.0502

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.109

Alfa AF: 0.135 Hom.: 600

Bravo AF: 0.135

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.1
Dann	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs202906; hg19: chr6-28011652;