rs1008138

Variant names:

• chr9-114047190-C-A
• rs1008138
• NM_001318042.2:c.1247-703C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-114047190-C-A
• chr9-114047190-C-G

Variant summary

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

The NM_001318042.2(ZNF618):​c.1247-703C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,016 control chromosomes in the GnomAD database, including 21,090 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 0.51 (21090 hom., cov: 33)
• Consequence: ZNF618 NM_001318042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF618	NM_001318042.2	c.1247-703C>A		intron_variant	Intron 13 of 14	ENST00000374126.10	NP_001304971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF618	ENST00000374126.10	c.1247-703C>A		intron_variant	Intron 13 of 14	1	NM_001318042.2	ENSP00000363241.5
ZNF618	ENST00000615615.4	c.1148-703C>A		intron_variant	Intron 12 of 13	1		ENSP00000483198.1
ZNF618	ENST00000470105.1	n.1260-703C>A		intron_variant	Intron 4 of 5	1
ZNF618	ENST00000288466.11	c.968-703C>A		intron_variant	Intron 12 of 13	2		ENSP00000288466.7

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77776 AN: 151898 Hom.: 21070 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.512 AC: 77841 AN: 152016 Hom.: 21090 Cov.: 33 AF XY: 0.513 AC XY: 38101 AN XY: 74322

African (AFR) AF: 0.679 AC: 28171 AN: 41464

American (AMR) AF: 0.434 AC: 6638 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3451 AN: 5176

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5843 AN: 10562

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29424 AN: 67932

Other (OTH) AF: 0.448 AC: 945 AN: 2110

Alfa AF: 0.460 Hom.: 45867

Bravo AF: 0.513

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.52
PhyloP100		-0.46
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: rs1008138; hg19: chr9-116809470;