chr19-53145820-A-G

Variant names:

• chr19-53145820-A-G
• rs10423215
• NM_032584.3:c.271+2861T>C

Variant summary

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

The NM_032584.3(ZNF347):​c.271+2861T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 151,874 control chromosomes in the GnomAD database, including 57,409 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 0.87 (57409 hom., cov: 29)
• Consequence: ZNF347 NM_032584.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

Genes affected

ZNF347 (HGNC:16447): (zinc finger protein 347) 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 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF347	NM_032584.3	c.271+2861T>C		intron_variant	Intron 4 of 4	ENST00000334197.12	NP_115973.2
ZNF347	NM_001172674.2	c.274+2861T>C		intron_variant	Intron 4 of 4		NP_001166145.1
ZNF347	NM_001172675.2	c.274+2861T>C		intron_variant	Intron 4 of 4		NP_001166146.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF347	ENST00000334197.12	c.271+2861T>C		intron_variant	Intron 4 of 4	1	NM_032584.3	ENSP00000334146.6

Frequencies

GnomAD3 genomes AF: 0.869 AC: 131874 AN: 151756 Hom.: 57358 Cov.: 29

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.869 AC: 131984 AN: 151874 Hom.: 57409 Cov.: 29 AF XY: 0.870 AC XY: 64606 AN XY: 74256

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.833

Alfa AF: 0.872 Hom.: 77181

Bravo AF: 0.866

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.47

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: rs10423215; hg19: chr19-53649073;