10-75269804-G-T

Position:

• chr10-75269804-G-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+24368G>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 0.328 in 192,928 control chromosomes in the GnomAD database, including 12,894 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 0.35 (11393 hom., cov: 31)
  • Exomes 𝑓: 0.26 (1501 hom.)
• Consequence: ZNF503-AS1 ENST00000666247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF503-AS1	ENST00000666247.1	n.291+24368G>T		intron_variant, non_coding_transcript_variant
ZNF503-AS1	ENST00000668612.1	n.17G>T		non_coding_transcript_exon_variant	1/3
ZNF503-AS1	ENST00000671219.1	n.24G>T		non_coding_transcript_exon_variant	1/4
ZNF503-AS1	ENST00000524517.5			upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52653 AN: 151826 Hom.: 11356 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.258 AC: 10558 AN: 40984 Hom.: 1501 Cov.: 0 AF XY: 0.264 AC XY: 5761 AN XY: 21792

Gnomad4 AFR exome AF: 0.579

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.267

Gnomad4 EAS exome AF: 0.0859

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.347 AC: 52731 AN: 151944 Hom.: 11393 Cov.: 31 AF XY: 0.339 AC XY: 25147 AN XY: 74284

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.365

Alfa AF: 0.180 Hom.: 422

Bravo AF: 0.362

Asia WGS AF: 0.266 AC: 923 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	0.29
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12253226; hg19: chr10-77029562;