chr19-52029018-C-T

Position:

• chr19-52029018-C-T

Variant summary

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

The XR_002958414.2(LOC112268244):​n.2047C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,172 control chromosomes in the GnomAD database, including 2,184 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 0.15 (2184 hom., cov: 32)
• Consequence: LOC112268244 XR_002958414.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

Genes affected

LOC112268244 (HGNC:):

ZNF614 (HGNC:24722): (zinc finger protein 614) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268244	XR_002958414.2	n.2047C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF614	ENST00000597952.1	c.-217+838G>A		intron_variant		3		ENSP00000469809

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22369 AN: 152054 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.147 AC: 22396 AN: 152172 Hom.: 2184 Cov.: 32 AF XY: 0.152 AC XY: 11305 AN XY: 74372

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.159

Alfa AF: 0.168 Hom.: 1268

Bravo AF: 0.144

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2288884; hg19: chr19-52532271;