NM_001306089.2:c.5113-202C>T

Variant names:

• chr18-76959485-C-T
• rs470563
• NM_001306089.2:c.5113-202C>T

Variant summary

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

The NM_001306089.2(ZNF236):​c.5113-202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,012 control chromosomes in the GnomAD database, including 20,326 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 0.49 (20326 hom., cov: 32)
• Consequence: ZNF236 NM_001306089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF236	NM_001306089.2	c.5113-202C>T		intron_variant	Intron 28 of 30	ENST00000320610.14	NP_001293018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF236	ENST00000320610.14	c.5113-202C>T		intron_variant	Intron 28 of 30	1	NM_001306089.2	ENSP00000322361.9
ZNF236	ENST00000253159.12	c.5107-202C>T		intron_variant	Intron 28 of 30	1		ENSP00000253159.8
ZNF236	ENST00000543926.6	n.*512-202C>T		intron_variant	Intron 29 of 31	1		ENSP00000444524.2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74915 AN: 151894 Hom.: 20321 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.493 AC: 74934 AN: 152012 Hom.: 20326 Cov.: 32 AF XY: 0.493 AC XY: 36599 AN XY: 74296

African (AFR) AF: 0.253 AC: 10475 AN: 41478

American (AMR) AF: 0.533 AC: 8156 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2658 AN: 5166

South Asian (SAS) AF: 0.528 AC: 2535 AN: 4802

European-Finnish (FIN) AF: 0.602 AC: 6356 AN: 10564

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41211 AN: 67926

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.571 Hom.: 12837

Bravo AF: 0.475

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		0.11
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: rs470563; hg19: chr18-74671441; COSMIC: COSV53501332;