rs2030008

chr6-28040470-G-T

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):n.188+19908C>A 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 0.0516 in 152,092 control chromosomes in the GnomAD database, including 294 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 0.052 (294 hom., cov: 32)
• Consequence: ZSCAN16-AS1 ENST00000660873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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+19908C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7811 AN: 151974 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0516 AC: 7848 AN: 152092 Hom.: 294 Cov.: 32 AF XY: 0.0549 AC XY: 4079 AN XY: 74360

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.0506

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0485 Hom.: 23

Bravo AF: 0.0453

Asia WGS AF: 0.171 AC: 593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.18
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030008; hg19: chr6-28008248;