NM_001306089.2:c.5243-360T>C

Variant names:

• chr18-76960319-T-C
• rs470337
• NM_001306089.2:c.5243-360T>C

Variant summary

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

The NM_001306089.2(ZNF236):​c.5243-360T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,170 control chromosomes in the GnomAD database, including 49,399 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 0.80 (49399 hom., cov: 32)
• Consequence: ZNF236 NM_001306089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 3 publications found

Genes affected

ZNF236 (HGNC:13028): (zinc finger protein 236) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to glucose stimulus. Predicted to be active in nucleus. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306089.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF236	NM_001306089.2	MANE Select	c.5243-360T>C		intron	N/A	NP_001293018.1
	ZNF236	NM_007345.4		c.5237-360T>C		intron	N/A	NP_031371.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF236	ENST00000320610.14	TSL:1 MANE Select	c.5243-360T>C		intron	N/A	ENSP00000322361.9
	ZNF236	ENST00000253159.12	TSL:1	c.5237-360T>C		intron	N/A	ENSP00000253159.8
	ZNF236	ENST00000543926.6	TSL:1	n.*642-360T>C		intron	N/A	ENSP00000444524.2

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122266 AN: 152052 Hom.: 49389 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.804 AC: 122316 AN: 152170 Hom.: 49399 Cov.: 32 AF XY: 0.802 AC XY: 59626 AN XY: 74386

African (AFR) AF: 0.706 AC: 29297 AN: 41486

American (AMR) AF: 0.878 AC: 13437 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2735 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4111 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3884 AN: 4824

European-Finnish (FIN) AF: 0.813 AC: 8623 AN: 10600

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57493 AN: 68008

Other (OTH) AF: 0.820 AC: 1733 AN: 2114

Alfa AF: 0.837 Hom.: 80747

Bravo AF: 0.803

Asia WGS AF: 0.791 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.56
PhyloP100		1.1
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: rs470337; hg19: chr18-74672275;