ENST00000395900.1:n.1342G>A

Variant names:

• chr11-32438918-G-A
• rs6508
• ENST00000395900.1:n.1342G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000395900.1(WT1-AS):​n.1342G>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 0.0978 in 534,676 control chromosomes in the GnomAD database, including 5,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (3318 hom., cov: 33)
  • Exomes 𝑓: 0.076 (1736 hom.)
• Consequence: WT1-AS ENST00000395900.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.315
• Publications: 9 publications found

Genes affected

WT1-AS (HGNC:18135): (WT1 antisense RNA) This gene is located upstream of the Wilms tumor 1 (WT1) gene; these two genes are bi-directionally transcribed from the same promoter region. This gene is imprinted in kidney, with preferential expression from the paternal allele. Imprinting defects at chromosome 11p13 may contribute to tumorigenesis. [provided by RefSeq, May 2014]

ENSG00000276530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 11-32438918-G-A is Benign according to our data. Variant chr11-32438918-G-A is described in ClinVar as Benign. ClinVar VariationId is 1166184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000395900.1. 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
	WT1-AS	NR_120546.1		n.1873G>A		non_coding_transcript_exon	Exon 2 of 2
	WT1-AS	NR_120547.1		n.1531G>A		non_coding_transcript_exon	Exon 3 of 3
	WT1-AS	NR_120548.1		n.329+3072G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WT1-AS	ENST00000395900.1	TSL:2	n.1342G>A		non_coding_transcript_exon	Exon 2 of 2
	WT1-AS	ENST00000442957.1	TSL:3	n.268G>A		non_coding_transcript_exon	Exon 2 of 2
	WT1-AS	ENST00000494911.6	TSL:4	n.1531G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23364 AN: 152114 Hom.: 3308 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.132

GnomAD2 exomes AF: 0.0828 AC: 20820 AN: 251372 AF XY: 0.0774

Gnomad AFR exome AF: 0.385

Gnomad AMR exome AF: 0.0551

Gnomad ASJ exome AF: 0.0840

Gnomad EAS exome AF: 0.00261

Gnomad FIN exome AF: 0.0532

Gnomad NFE exome AF: 0.0689

Gnomad OTH exome AF: 0.0774

GnomAD4 exome AF: 0.0756 AC: 28901 AN: 382444 Hom.: 1736 Cov.: 0 AF XY: 0.0743 AC XY: 16174 AN XY: 217716

African (AFR) AF: 0.380 AC: 4000 AN: 10514

American (AMR) AF: 0.0563 AC: 2042 AN: 36300

Ashkenazi Jewish (ASJ) AF: 0.0837 AC: 983 AN: 11744

East Asian (EAS) AF: 0.00486 AC: 64 AN: 13176

South Asian (SAS) AF: 0.0801 AC: 5345 AN: 66756

European-Finnish (FIN) AF: 0.0529 AC: 1710 AN: 32318

Middle Eastern (MID) AF: 0.114 AC: 325 AN: 2854

European-Non Finnish (NFE) AF: 0.0679 AC: 13034 AN: 192054

Other (OTH) AF: 0.0836 AC: 1398 AN: 16728

GnomAD4 genome AF: 0.154 AC: 23415 AN: 152232 Hom.: 3318 Cov.: 33 AF XY: 0.150 AC XY: 11183 AN XY: 74444

African (AFR) AF: 0.379 AC: 15721 AN: 41520

American (AMR) AF: 0.0904 AC: 1383 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5180

South Asian (SAS) AF: 0.0683 AC: 330 AN: 4830

European-Finnish (FIN) AF: 0.0547 AC: 580 AN: 10612

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4734 AN: 68006

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.104 Hom.: 2615

Bravo AF: 0.165

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

11p partial monosomy syndrome;C0950121:Drash syndrome;C0950122:Frasier syndrome;CN033288:Wilms tumor 1 Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not provided Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6508; hg19: chr11-32460464;