10-75262703-C-T

Variant names:

• chr10-75262703-C-T
• rs12766938
• ENST00000734866.1:n.17C>T

Variant summary

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

The ENST00000734866.1(ZNF503-AS1):​n.17C>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 0.082 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 ENST00000734866.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734866.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF503-AS1	ENST00000734866.1		n.17C>T		non_coding_transcript_exon	Exon 1 of 3
	ZNF503-AS1	ENST00000666247.1		n.291+17267C>T		intron	N/A
	ZNF503-AS1	ENST00000734865.1		n.311+17267C>T		intron	N/A

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

African (AFR) AF: 0.0316 AC: 999 AN: 31624

American (AMR) AF: 0.114 AC: 1078 AN: 9434

Ashkenazi Jewish (ASJ) AF: 0.0940 AC: 311 AN: 3308

East Asian (EAS) AF: 0.0557 AC: 191 AN: 3432

South Asian (SAS) AF: 0.275 AC: 1052 AN: 3832

European-Finnish (FIN) AF: 0.0542 AC: 255 AN: 4708

Middle Eastern (MID) AF: 0.143 AC: 26 AN: 182

European-Non Finnish (NFE) AF: 0.0932 AC: 5868 AN: 62942

Other (OTH) AF: 0.108 AC: 182 AN: 1692

Alfa AF: 0.0774 Hom.: 849

Bravo AF: 0.0647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.016
DANN	Benign	0.80
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs12766938; hg19: chr10-77022461;