rs149990

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 (AMR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN16-AS1	ENST00000660873.1	n.189-13279C>T		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.102

Alfa AF: 0.117 Hom.: 1308

Bravo AF: 0.125

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149990; hg19: chr6-27998258;