6-28040470-G-T

Variant names:

• chr6-28040470-G-T
• rs2030008
• ENST00000660873.1:n.188+19908C>A

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+19908C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.144 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.188+19908C>A		intron	N/A
	ZSCAN16-AS1	ENST00000716089.1		n.223+19908C>A		intron	N/A
	ZSCAN16-AS1	ENST00000716090.1		n.310+19908C>A		intron	N/A

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

African (AFR) AF: 0.0196 AC: 813 AN: 41512

American (AMR) AF: 0.0646 AC: 987 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 512 AN: 5162

South Asian (SAS) AF: 0.153 AC: 739 AN: 4822

European-Finnish (FIN) AF: 0.0981 AC: 1036 AN: 10556

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0506 AC: 3438 AN: 67980

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0471 Hom.: 24

Bravo AF: 0.0453

Asia WGS AF: 0.171 AC: 593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.51
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2030008; hg19: chr6-28008248;