chr10-75269804-G-T

Variant names:

• chr10-75269804-G-T
• rs12253226
• ENST00000668612.1:n.17G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668612.1(ZNF503-AS1):​n.17G>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 0.328 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 ENST00000668612.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF503-AS1	ENST00000668612.1	n.17G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ZNF503-AS1	ENST00000671219.1	n.24G>T		non_coding_transcript_exon_variant	Exon 1 of 4
ZNF503-AS1	ENST00000666247.1	n.291+24368G>T		intron_variant	Intron 2 of 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

African (AFR) AF: 0.579 AC: 836 AN: 1444

American (AMR) AF: 0.208 AC: 548 AN: 2640

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 289 AN: 1084

East Asian (EAS) AF: 0.0859 AC: 218 AN: 2538

South Asian (SAS) AF: 0.361 AC: 1632 AN: 4518

European-Finnish (FIN) AF: 0.133 AC: 219 AN: 1642

Middle Eastern (MID) AF: 0.356 AC: 62 AN: 174

European-Non Finnish (NFE) AF: 0.252 AC: 6235 AN: 24762

Other (OTH) AF: 0.238 AC: 519 AN: 2182

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

African (AFR) AF: 0.598 AC: 24759 AN: 41398

American (AMR) AF: 0.261 AC: 3979 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 958 AN: 3464

East Asian (EAS) AF: 0.0970 AC: 501 AN: 5166

South Asian (SAS) AF: 0.400 AC: 1923 AN: 4808

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10578

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18204 AN: 67964

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.296 Hom.: 11048

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12253226; hg19: chr10-77029562;