6-28043874-T-C

Variant names:

• chr6-28043874-T-C
• rs202906
• ENST00000660873.1:n.188+16504A>G

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):​n.188+16504A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 30 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN16-AS1	ENST00000660873.1		n.188+16504A>G		intron	N/A
	ZSCAN16-AS1	ENST00000716089.1		n.223+16504A>G		intron	N/A
	ZSCAN16-AS1	ENST00000716090.1		n.310+16504A>G		intron	N/A

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

African (AFR) AF: 0.162 AC: 6703 AN: 41464

American (AMR) AF: 0.142 AC: 2167 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.119 AC: 615 AN: 5148

South Asian (SAS) AF: 0.0935 AC: 450 AN: 4814

European-Finnish (FIN) AF: 0.0502 AC: 532 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8230 AN: 67980

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.141 Hom.: 1681

Bravo AF: 0.135

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.86
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs202906; hg19: chr6-28011652;