11-65569348-C-T

Variant names:

• chr11-65569348-C-T
• rs3782089
• ENST00000623234.3:n.1485G>A

Variant summary

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

The ENST00000623234.3(ZNRD2-DT):​n.1485G>A 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 0.0586 in 153,240 control chromosomes in the GnomAD database, including 323 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 0.058 (317 hom., cov: 33)
  • Exomes 𝑓: 0.076 (6 hom.)
• Consequence: ZNRD2-DT ENST00000623234.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 56 publications found

Genes affected

ZNRD2-DT (HGNC:27384): (ZNRD2 divergent transcript)

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 (SAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNRD2-DT	NR_038923.1	n.1066G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNRD2-DT	ENST00000623234.3	n.1485G>A		non_coding_transcript_exon_variant	Exon 3 of 3	6
ZNRD2-DT	ENST00000725955.1	n.969G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ZNRD2-DT	ENST00000725946.1	n.673+348G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8910 AN: 152114 Hom.: 318 Cov.: 33

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0568

GnomAD4 exome AF: 0.0764 AC: 77 AN: 1008 Hom.: 6 Cov.: 0 AF XY: 0.0860 AC XY: 60 AN XY: 698

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.0250 AC: 1 AN: 40

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.104 AC: 51 AN: 492

European-Finnish (FIN) AF: 0.0227 AC: 1 AN: 44

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0615 AC: 23 AN: 374

Other (OTH) AF: 0.0208 AC: 1 AN: 48

GnomAD4 genome AF: 0.0585 AC: 8903 AN: 152232 Hom.: 317 Cov.: 33 AF XY: 0.0592 AC XY: 4403 AN XY: 74420

African (AFR) AF: 0.0335 AC: 1391 AN: 41546

American (AMR) AF: 0.0556 AC: 851 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.0301 AC: 156 AN: 5186

South Asian (SAS) AF: 0.151 AC: 725 AN: 4814

European-Finnish (FIN) AF: 0.0571 AC: 605 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4561 AN: 68002

Other (OTH) AF: 0.0567 AC: 120 AN: 2116

Alfa AF: 0.0629 Hom.: 918

Bravo AF: 0.0542

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.95
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3782089; hg19: chr11-65336819;