9-113963201-G-A

Variant names:

• chr9-113963201-G-A
• rs10817542
• NM_001318042.2:c.34-5916G>A

Variant summary

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

The NM_001318042.2(ZNF618):​c.34-5916G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,192 control chromosomes in the GnomAD database, including 3,056 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 0.18 (3056 hom., cov: 33)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318042.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	NM_001318042.2	MANE Select	c.34-5916G>A		intron	N/A	NP_001304971.1
	ZNF618	NM_001318041.2		c.34-5916G>A		intron	N/A	NP_001304970.1
	ZNF618	NM_001318040.2		c.34-5916G>A		intron	N/A	NP_001304969.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF618	ENST00000374126.10	TSL:1 MANE Select	c.34-5916G>A		intron	N/A	ENSP00000363241.5
	ZNF618	ENST00000615615.4	TSL:1	c.34-5916G>A		intron	N/A	ENSP00000483198.1
	ZNF618	ENST00000288466.11	TSL:2	c.34-5916G>A		intron	N/A	ENSP00000288466.7

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27090 AN: 152074 Hom.: 3060 Cov.: 33

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.178 AC: 27084 AN: 152192 Hom.: 3056 Cov.: 33 AF XY: 0.178 AC XY: 13223 AN XY: 74410

African (AFR) AF: 0.0474 AC: 1971 AN: 41554

American (AMR) AF: 0.204 AC: 3119 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1335 AN: 5166

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1927 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15423 AN: 67996

Other (OTH) AF: 0.194 AC: 410 AN: 2114

Alfa AF: 0.219 Hom.: 6166

Bravo AF: 0.174

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.89
DANN	Benign	0.54
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10817542; hg19: chr9-116725481;