19-51942133-T-C

Position:

• chr19-51942133-T-C

Variant summary

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

The NM_001031721.4(ZNF613):​c.235+1424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,162 control chromosomes in the GnomAD database, including 5,656 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 0.23 (5656 hom., cov: 32)
• Consequence: ZNF613 NM_001031721.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

ZNF613 (HGNC:25827): (zinc finger protein 613) Predicted to enable DNA-binding transcription factor activity 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF613	NM_001031721.4	c.235+1424T>C		intron_variant		ENST00000293471.11
ZNF613	NM_024840.4	c.127+1424T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF613	ENST00000293471.11	c.235+1424T>C		intron_variant		1	NM_001031721.4	P1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34972 AN: 152042 Hom.: 5634 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.230 AC: 35040 AN: 152162 Hom.: 5656 Cov.: 32 AF XY: 0.231 AC XY: 17164 AN XY: 74390

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.235

Alfa AF: 0.158 Hom.: 1364

Bravo AF: 0.240

Asia WGS AF: 0.219 AC: 763 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.28

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: rs8113308; hg19: chr19-52445386;