rs172166

Positions:

• chr6-28053042-C-G
• chr6-28053042-C-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+7336G>C 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 0.253 in 151,506 control chromosomes in the GnomAD database, including 5,456 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 0.25 (5456 hom., cov: 31)
• Consequence: ZSCAN16-AS1 ENST00000660873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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+7336G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38310 AN: 151388 Hom.: 5446 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.253 AC: 38354 AN: 151506 Hom.: 5456 Cov.: 31 AF XY: 0.246 AC XY: 18234 AN XY: 74044

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.243

Alfa AF: 0.221 Hom.: 550

Bravo AF: 0.269

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs172166; hg19: chr6-28020820;