rs750561326

Variant names:

• chr18-35337626-C-A
• rs750561326
• NM_006965.4:c.713G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-35337626-C-A
• chr18-35337626-C-G
• chr18-35337626-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006965.4(ZNF24):​c.713G>T​(p.Arg238Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R238T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF24 NM_006965.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

Genes affected

ZNF24 (HGNC:13032): (zinc finger protein 24) Enables DNA-binding transcription activator activity, RNA polymerase II-specific; identical protein binding activity; and sequence-specific DNA binding activity. Involved in negative regulation of transcription, DNA-templated and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF24	NM_006965.4	c.713G>T	p.Arg238Met	missense_variant	Exon 4 of 4	ENST00000261332.11	NP_008896.2
ZNF24	NM_001375815.1	c.713G>T	p.Arg238Met	missense_variant	Exon 4 of 4		NP_001362744.1
ZNF24	NM_001308123.2	c.*1434G>T		3_prime_UTR_variant	Exon 4 of 4		NP_001295052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF24	ENST00000261332.11	c.713G>T	p.Arg238Met	missense_variant	Exon 4 of 4	1	NM_006965.4	ENSP00000261332.5
ZNF24	ENST00000399061.3	c.713G>T	p.Arg238Met	missense_variant	Exon 4 of 4	1		ENSP00000382015.2
ZNF24	ENST00000589881	c.*1434G>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000467655.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Uncertain	24
DANN	Benign	0.96
DEOGEN2	Uncertain	0.45	T;T
Eigen	Uncertain	0.25
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Benign	0.31	N
LIST_S2	Benign	0.24	.;T
M_CAP	Benign	0.0050	T
MetaRNN	Uncertain	0.60	D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Benign	0.47	T
PROVEAN	Uncertain	-4.2	D;D
REVEL	Benign	0.14
Sift	Uncertain	0.0020	D;D
Sift4G	Uncertain	0.0070	D;D
Polyphen		0.98	D;D
Vest4		0.58
MutPred		0.50		Loss of MoRF binding (P = 0.0555);Loss of MoRF binding (P = 0.0555);
MVP		0.24
MPC		0.96
ClinPred		0.97	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.25
gMVP		0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs750561326; hg19: chr18-32917590;