10-30884865-T-C

Variant names:

• chr10-30884865-T-C
• rs2172659
• NM_001143768.2:c.-31-7800A>G

Variant summary

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

The NM_001143768.2(ZNF438):​c.-31-7800A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,162 control chromosomes in the GnomAD database, including 47,125 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 0.78 (47125 hom., cov: 32)
• Consequence: ZNF438 NM_001143768.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

Genes affected

ZNF438 (HGNC:21029): (zinc finger protein 438) Enables DNA-binding transcription factor activity. Involved in negative regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143768.2. 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
	ZNF438	NM_001143768.2	MANE Select	c.-31-7800A>G		intron	N/A	NP_001137240.1	Q7Z4V0-1
	ZNF438	NM_001143766.2		c.-31-7800A>G		intron	N/A	NP_001137238.1	Q7Z4V0-1
	ZNF438	NM_001143767.2		c.-31-7800A>G		intron	N/A	NP_001137239.1	Q7Z4V0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF438	ENST00000436087.7	TSL:5 MANE Select	c.-31-7800A>G		intron	N/A	ENSP00000406934.2	Q7Z4V0-1
	ZNF438	ENST00000361310.7	TSL:1	c.-31-7800A>G		intron	N/A	ENSP00000354663.3	Q7Z4V0-1
	ZNF438	ENST00000331737.10	TSL:1	c.-160-7800A>G		intron	N/A	ENSP00000333571.6	Q7Z4V0-2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118617 AN: 152044 Hom.: 47073 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.780 AC: 118731 AN: 152162 Hom.: 47125 Cov.: 32 AF XY: 0.776 AC XY: 57718 AN XY: 74380

African (AFR) AF: 0.891 AC: 37025 AN: 41536

American (AMR) AF: 0.732 AC: 11193 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2246 AN: 5172

South Asian (SAS) AF: 0.605 AC: 2915 AN: 4822

European-Finnish (FIN) AF: 0.780 AC: 8247 AN: 10578

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52281 AN: 67976

Other (OTH) AF: 0.746 AC: 1577 AN: 2114

Alfa AF: 0.778 Hom.: 5691

Bravo AF: 0.781

Asia WGS AF: 0.575 AC: 2000 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-1.4
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: rs2172659; hg19: chr10-31173794;