Genetic Variant ENSG00000291008:n.471T>C (chr6-28092461-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000529104.2(ENSG00000291008):n.471T>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
ENST00000529104.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.590

Variant links:

Genes affected

ENSG00000291008 (HGNC:):

ENSG00000291008 links:

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

ZSCAN12P1 links:

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ZSCAN16-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
ZSCAN12P1	NR_024063.2 link	n.801T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291008	ENST00000529104.2 link	n.471T>C	non_coding_transcript_exon_variant	Exon 2 of 2	1
ZSCAN12P1	ENST00000406489.2 link	n.35T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
ZSCAN16-AS1	ENST00000660873.1 link	n.78-31973A>G	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0505

AC:

7685

AN:

152094

Hom.:

310

Cov.:

show subpopulations

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:

AN:

526

Hom.:

Cov.:

AF XY:

0.0805

AC XY:

AN XY:

298

show subpopulations

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.:

AF XY:

0.0453

AC XY:

3374

AN XY:

74414

show subpopulations

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:

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over