chr6-28092461-T-C

Position:

• chr6-28092461-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024063.2(ZSCAN12P1):​n.801T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 152,738 control chromosomes in the GnomAD database, including 313 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 0.050 (310 hom., cov: 32)
  • Exomes 𝑓: 0.068 (3 hom.)
• Consequence: ZSCAN12P1 NR_024063.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

Genes affected

ZSCAN12P1 (HGNC:13850): (zinc finger and SCAN domain containing 12 pseudogene 1)

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN12P1	NR_024063.2	n.801T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN12P1	ENST00000406489.2	n.35T>C		non_coding_transcript_exon_variant	1/1
	ENST00000529104.2	n.471T>C		non_coding_transcript_exon_variant	2/2	1
ZSCAN16-AS1	ENST00000660873.1	n.78-31973A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0505 AC: 7685 AN: 152094 Hom.: 310 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0354

GnomAD4 exome AF: 0.0684 AC: 36 AN: 526 Hom.: 3 Cov.: 0 AF XY: 0.0805 AC XY: 24 AN XY: 298

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0221

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.0938

GnomAD4 genome AF: 0.0505 AC: 7681 AN: 152212 Hom.: 310 Cov.: 32 AF XY: 0.0453 AC XY: 3374 AN XY: 74414

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0710 Hom.: 414

Bravo AF: 0.0482

Asia WGS AF: 0.00404 AC: 15 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	0.75
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13197574; hg19: chr6-28060239;