ENST00000660873.1:n.189-13279C>T

Variant names:

• chr6-28030480-G-A
• rs149990
• ENST00000660873.1:n.189-13279C>T

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):​n.189-13279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,140 control chromosomes in the GnomAD database, including 1,150 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 0.12 (1150 hom., cov: 32)
• Consequence: ZSCAN16-AS1 ENST00000660873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 23 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN16-AS1	ENST00000660873.1		n.189-13279C>T		intron	N/A
	ZSCAN16-AS1	ENST00000716089.1		n.224-21472C>T		intron	N/A
	ZSCAN16-AS1	ENST00000716090.1		n.311-21472C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18056 AN: 152022 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.119 AC: 18077 AN: 152140 Hom.: 1150 Cov.: 32 AF XY: 0.115 AC XY: 8547 AN XY: 74392

African (AFR) AF: 0.135 AC: 5610 AN: 41506

American (AMR) AF: 0.136 AC: 2084 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.120 AC: 622 AN: 5174

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4820

European-Finnish (FIN) AF: 0.0496 AC: 525 AN: 10592

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8175 AN: 67992

Other (OTH) AF: 0.102 AC: 216 AN: 2110

Alfa AF: 0.123 Hom.: 3665

Bravo AF: 0.125

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.35
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs149990; hg19: chr6-27998258;