19-44109508-A-C

Variant names:

• chr19-44109508-A-C
• rs2061332
• NM_001321645.3:c.*1224A>C

Variant summary

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

The NM_001321645.3(ZNF224):​c.*1224A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,892 control chromosomes in the GnomAD database, including 35,190 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 0.64 (35189 hom., cov: 30)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ZNF224 NM_001321645.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 15 publications found

Genes affected

ZNF224 (HGNC:13017): (zinc finger protein 224) This gene encodes a member of the Krueppel C2H2-type zinc-finger family of proteins. The encoded protein represses transcription of the aldolase A gene, which encodes a key enzyme in glycolysis. The encoded zinc-finger protein may also function as a transcriptional co-activator with Wilms' tumor protein 1 to regulate apoptotic genes in leukemia. [provided by RefSeq, Jul 2016]

ZNF225-AS1 (HGNC:55916): (ZNF225 and ZNF224 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF224	NM_001321645.3	c.*1224A>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000693561.1	NP_001308574.1
ZNF224	NM_013398.5	c.*1224A>C		3_prime_UTR_variant	Exon 6 of 6		NP_037530.2
ZNF225-AS1	NR_033341.1	n.363-1171T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF224	ENST00000693561.1	c.*1224A>C		3_prime_UTR_variant	Exon 6 of 6		NM_001321645.3	ENSP00000508532.1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97944 AN: 151772 Hom.: 35185 Cov.: 30

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.696

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.645 AC: 97962 AN: 151890 Hom.: 35189 Cov.: 30 AF XY: 0.640 AC XY: 47463 AN XY: 74208

African (AFR) AF: 0.337 AC: 13941 AN: 41408

American (AMR) AF: 0.553 AC: 8425 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2841 AN: 5160

South Asian (SAS) AF: 0.682 AC: 3287 AN: 4818

European-Finnish (FIN) AF: 0.771 AC: 8125 AN: 10532

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56289 AN: 67966

Other (OTH) AF: 0.694 AC: 1463 AN: 2108

Alfa AF: 0.749 Hom.: 105784

Bravo AF: 0.614

Asia WGS AF: 0.580 AC: 2018 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		0.64

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: rs2061332; hg19: chr19-44613661;