rs6013382

Positions:

• chr20-52086094-C-T

Variant summary

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

The ENST00000665639.1(ENSG00000287511):​n.186+2532C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,030 control chromosomes in the GnomAD database, including 17,846 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 0.48 (17846 hom., cov: 33)
• Consequence: ENST00000665639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

ZFP64 (HGNC:15940): (ZFP64 zinc finger protein) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in positive regulation of cytokine production and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of mRNA splicing, via spliceosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372664	XR_936849.3	n.6519+2532C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665639.1	n.186+2532C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72957 AN: 151912 Hom.: 17828 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.480 AC: 73020 AN: 152030 Hom.: 17846 Cov.: 33 AF XY: 0.479 AC XY: 35562 AN XY: 74308

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.423

Alfa AF: 0.460 Hom.: 35199

Bravo AF: 0.471

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs6013382; hg19: chr20-50702633;