10-45147086-G-A

Variant names:

• chr10-45147086-G-A
• rs1339746
• ENST00000448600.5:n.90-141C>T

Variant summary

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

The ENST00000448600.5(ZNF22-AS1):​n.90-141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 162,038 control chromosomes in the GnomAD database, including 73,974 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 0.95 (69497 hom., cov: 34)
  • Exomes 𝑓: 0.96 (4477 hom.)
• Consequence: ZNF22-AS1 ENST00000448600.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 2 publications found

Genes affected

ZNF22-AS1 (HGNC:23509): (ZNF22 antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

CUBNP3 (HGNC:44985): (cubilin pseudogene 3)

RSU1P2 (HGNC:44391): (Ras suppressor protein 1 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448600.5. 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
	RSU1P2	NR_024472.1		n.263-141C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF22-AS1	ENST00000448600.5	TSL:1	n.90-141C>T		intron	N/A
	ZNF22-AS1	ENST00000619977.1	TSL:1	n.263-141C>T		intron	N/A
	ZNF22-AS1	ENST00000599308.3	TSL:5	n.136C>T		non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145329 AN: 152238 Hom.: 69435 Cov.: 34

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.951

GnomAD4 exome AF: 0.961 AC: 9306 AN: 9682 Hom.: 4477 Cov.: 0 AF XY: 0.958 AC XY: 4838 AN XY: 5048

African (AFR) AF: 0.987 AC: 377 AN: 382

American (AMR) AF: 0.977 AC: 1341 AN: 1372

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 220 AN: 228

East Asian (EAS) AF: 1.00 AC: 710 AN: 710

South Asian (SAS) AF: 0.991 AC: 664 AN: 670

European-Finnish (FIN) AF: 0.896 AC: 138 AN: 154

Middle Eastern (MID) AF: 0.944 AC: 34 AN: 36

European-Non Finnish (NFE) AF: 0.950 AC: 5327 AN: 5606

Other (OTH) AF: 0.945 AC: 495 AN: 524

GnomAD4 genome AF: 0.955 AC: 145450 AN: 152356 Hom.: 69497 Cov.: 34 AF XY: 0.955 AC XY: 71124 AN XY: 74490

African (AFR) AF: 0.988 AC: 41107 AN: 41590

American (AMR) AF: 0.959 AC: 14683 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5192 AN: 5196

South Asian (SAS) AF: 0.983 AC: 4750 AN: 4830

European-Finnish (FIN) AF: 0.923 AC: 9785 AN: 10602

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63599 AN: 68038

Other (OTH) AF: 0.952 AC: 2014 AN: 2116

Alfa AF: 0.942 Hom.: 23057

Bravo AF: 0.960

Asia WGS AF: 0.988 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.58
DANN	Benign	0.86
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs1339746; hg19: chr10-45642534;