rs2172659

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-30884865-T-A
• chr10-30884865-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001143768.2(ZNF438):​c.-31-7800A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF438	NM_001143768.2	MANE Select	c.-31-7800A>T		intron	N/A	NP_001137240.1
	ZNF438	NM_001143766.2		c.-31-7800A>T		intron	N/A	NP_001137238.1
	ZNF438	NM_001143767.2		c.-31-7800A>T		intron	N/A	NP_001137239.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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;