19-44175793-C-T

Variant names:

• chr19-44175793-C-T
• rs1284269453
• NM_001032373.2:c.531C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001032373.2(ZNF226):​c.531C>T​(p.Phe177Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,461,376 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 0.000022 (0 hom.)
• Consequence: ZNF226 NM_001032373.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 0 publications found

Genes affected

ZNF226 (HGNC:13019): (zinc finger protein 226) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP7: Synonymous conserved (PhyloP=-0.841 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032373.2. 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
	ZNF226	NM_001032373.2	MANE Select	c.531C>T	p.Phe177Phe	synonymous	Exon 6 of 6	NP_001027545.1	Q9NYT6-1
	ZNF226	NM_001032372.2		c.531C>T	p.Phe177Phe	synonymous	Exon 6 of 6	NP_001027544.1	Q9NYT6-1
	ZNF226	NM_001319088.2		c.531C>T	p.Phe177Phe	synonymous	Exon 6 of 6	NP_001306017.1	Q9NYT6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF226	ENST00000337433.10	TSL:1 MANE Select	c.531C>T	p.Phe177Phe	synonymous	Exon 6 of 6	ENSP00000336719.5	Q9NYT6-1
	ZNF226	ENST00000454662.6	TSL:1	c.531C>T	p.Phe177Phe	synonymous	Exon 6 of 6	ENSP00000393265.1	Q9NYT6-1
	ZNF226	ENST00000590089.5	TSL:1	c.531C>T	p.Phe177Phe	synonymous	Exon 7 of 7	ENSP00000465121.1	Q9NYT6-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000404 AC: 1 AN: 247684 AF XY: 0.00000743

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000893

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000219 AC: 32 AN: 1461376 Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15 AN XY: 726950

African (AFR) AF: 0.00 AC: 0 AN: 33476

American (AMR) AF: 0.00 AC: 0 AN: 44688

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39684

South Asian (SAS) AF: 0.00 AC: 0 AN: 86184

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53340

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000270 AC: 30 AN: 1111750

Other (OTH) AF: 0.0000331 AC: 2 AN: 60360

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.96
DANN	Benign	0.52
PhyloP100		-0.84

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: rs1284269453; hg19: chr19-44679946; COSMIC: COSV100335247; COSMIC: COSV100335247;