rs1408113

Positions:

• chr9-113980553-A-G
• chr9-113980553-A-T

Variant summary

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

The NM_001318042.2(ZNF618):​c.78-7768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,032 control chromosomes in the GnomAD database, including 24,690 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 0.57 (24690 hom., cov: 32)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.78-7768A>G		intron_variant		ENST00000374126.10	NP_001304971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF618	ENST00000374126.10	c.78-7768A>G		intron_variant		1	NM_001318042.2	ENSP00000363241	P4

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86063 AN: 151914 Hom.: 24683 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.613

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.566 AC: 86108 AN: 152032 Hom.: 24690 Cov.: 32 AF XY: 0.564 AC XY: 41932 AN XY: 74328

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.616

Alfa AF: 0.554 Hom.: 2779

Bravo AF: 0.571

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.44

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

Other links and lift over

dbSNP: rs1408113; hg19: chr9-116742833;