chr19-36906399-C-T

Position:

• chr19-36906399-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037232.4(ZNF829):​c.319+1530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,038 control chromosomes in the GnomAD database, including 1,642 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 0.14 (1642 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF829 NM_001037232.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ZNF829 (HGNC:34032): (zinc finger protein 829) Predicted to enable DNA-binding transcription factor 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF345 (HGNC:16367): (zinc finger protein 345) Enables sequence-specific double-stranded 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF829	NM_001037232.4	c.319+1530G>A		intron_variant		ENST00000391711.8	NP_001032309.2
ZNF829	NM_001171979.2	c.562+1530G>A		intron_variant			NP_001165450.1
ZNF829	XM_005258876.4	c.319+1530G>A		intron_variant			XP_005258933.1
ZNF829	XM_011526933.3	c.319+1530G>A		intron_variant			XP_011525235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF829	ENST00000391711.8	c.319+1530G>A		intron_variant		1	NM_001037232.4	ENSP00000429266	P2
ZNF829	ENST00000520965.5	c.562+1530G>A		intron_variant		1		ENSP00000428679	A2
ZNF829	ENST00000520907.1	n.2214G>A		non_coding_transcript_exon_variant	5/5	2
ZNF345	ENST00000432005.6	n.283-6328C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20629 AN: 151920 Hom.: 1637 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0518

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.150

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.136 AC: 20657 AN: 152038 Hom.: 1642 Cov.: 32 AF XY: 0.136 AC XY: 10106 AN XY: 74334

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.0913

Gnomad4 OTH AF: 0.150

Alfa AF: 0.105 Hom.: 934

Bravo AF: 0.141

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.55

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: rs9304878; hg19: chr19-37397301;