6-28092461-T-C

Variant names:

• chr6-28092461-T-C
• rs13197574
• ENST00000529104.3:n.481T>C

Variant summary

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

The ENST00000529104.3(ENSG00000291008):​n.481T>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: ENSG00000291008 ENST00000529104.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 30 publications found

Genes affected

ENSG00000291008 (HGNC:):

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529104.3. 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
	ZSCAN12P1	NR_024063.2		n.801T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291008	ENST00000529104.3	TSL:1	n.481T>C		non_coding_transcript_exon	Exon 2 of 2
	ZSCAN12P1	ENST00000406489.2	TSL:6	n.35T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000291008	ENST00000733542.1		n.375T>C		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.00 AC: 0 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 14

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12

East Asian (EAS) AF: 0.00 AC: 0 AN: 24

South Asian (SAS) AF: 0.00 AC: 0 AN: 8

European-Finnish (FIN) AF: 0.0221 AC: 3 AN: 136

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.105 AC: 30 AN: 286

Other (OTH) AF: 0.0938 AC: 3 AN: 32

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

African (AFR) AF: 0.0174 AC: 722 AN: 41542

American (AMR) AF: 0.0237 AC: 363 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4822

European-Finnish (FIN) AF: 0.0396 AC: 419 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5912 AN: 67994

Other (OTH) AF: 0.0351 AC: 74 AN: 2110

Alfa AF: 0.0730 Hom.: 939

Bravo AF: 0.0482

Asia WGS AF: 0.00404 AC: 15 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	0.75
DANN	Benign	0.43
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13197574;

hg19: chr6-28060239;