10-75262703-C-T

Variant summary

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

The ENST00000666247.1(ZNF503-AS1):n.291+17267C>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 0.082 in 122,022 control chromosomes in the GnomAD database, including 459 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 0.082 (459 hom., cov: 28)
• Consequence: ZNF503-AS1 ENST00000666247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

Genes affected

ZNF503-AS1 (HGNC:27370): (ZNF503 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF503-AS1	ENST00000666247.1	n.291+17267C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 10005 AN: 121998 Hom.: 457 Cov.: 28

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0940

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0820 AC: 10005 AN: 122022 Hom.: 459 Cov.: 28 AF XY: 0.0868 AC XY: 4896 AN XY: 56378

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0940

Gnomad4 EAS AF: 0.0557

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0519 Hom.: 63

Bravo AF: 0.0647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.016
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12766938; hg19: chr10-77022461;