Genetic Variant ZNF618:c.551-115C>T (chr9-114007235-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001318042.2(ZNF618):c.551-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 801,416 control chromosomes in the GnomAD database, including 159,434 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 0.55 ( 24938 hom., cov: 31)

Exomes 𝑓: 0.64 ( 134496 hom. )

Consequence

ZNF618
NM_001318042.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Variant links:

Genes affected

ZNF618 (HGNC:29416): (zinc finger protein 618) Enables identical protein binding activity and transcription coregulator binding activity. Involved in positive regulation of chromatin binding activity. Located in chromatin. Part of pericentric heterochromatin. [provided by Alliance of Genome Resources, Apr 2022]

ZNF618 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF618	NM_001318042.2 link	c.551-115C>T		intron_variant	Intron 6 of 14	ENST00000374126.10	NP_001304971.1	Q5T7W0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF618	ENST00000374126.10 link	c.551-115C>T		intron_variant	Intron 6 of 14	1	NM_001318042.2	ENSP00000363241.5		Q5T7W0-1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83337

AN:

151878

Hom.:

24936

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.792

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.715

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.661

Gnomad OTH

AF:

0.535

GnomAD4 exome

AF:

0.639

AC:

415050

AN:

649420

Hom.:

134496

AF XY:

0.640

AC XY:

215847

AN XY:

337356

show subpopulations

Gnomad4 AFR exome

AF:

0.281

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.644

Gnomad4 EAS exome

AF:

0.674

Gnomad4 SAS exome

AF:

0.620

Gnomad4 FIN exome

AF:

0.713

Gnomad4 NFE exome

AF:

0.654

Gnomad4 OTH exome

AF:

0.605

GnomAD4 genome

AF:

0.548

AC:

83357

AN:

151996

Hom.:

24938

Cov.:

AF XY:

0.551

AC XY:

40966

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.293

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.636

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.715

Gnomad4 NFE

AF:

0.661

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.634

Hom.:

14264

Bravo

AF:

0.522

Asia WGS

AF:

0.567

AC:

1975

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.36

DANN

Benign

0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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