21-38911809-C-T

Position:

• chr21-38911809-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_120405.1(ETS2-AS1):​n.677-9844G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 152,324 control chromosomes in the GnomAD database, including 112 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 0.030 (112 hom., cov: 32)
• Consequence: ETS2-AS1 NR_120405.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

ETS2-AS1 (HGNC:56712): (ETS2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.03 (4575/152324) while in subpopulation NFE AF= 0.0463 (3150/68030). AF 95% confidence interval is 0.045. There are 112 homozygotes in gnomad4. There are 2072 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 112 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETS2-AS1	NR_120405.1	n.677-9844G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000380931.6	n.677-9844G>A		intron_variant, non_coding_transcript_variant		2
ETS2-AS1	ENST00000415824.1	n.277-9844G>A		intron_variant, non_coding_transcript_variant		5
ETS2-AS1	ENST00000626259.2	n.58+1055G>A		intron_variant, non_coding_transcript_variant		5
ETS2-AS1	ENST00000669345.1	n.2-9844G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4577 AN: 152206 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00835

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.0869

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0300 AC: 4575 AN: 152324 Hom.: 112 Cov.: 32 AF XY: 0.0278 AC XY: 2072 AN XY: 74482

Gnomad4 AFR AF: 0.00832

Gnomad4 AMR AF: 0.0254

Gnomad4 ASJ AF: 0.0869

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0362 Hom.: 13

Bravo AF: 0.0303

Asia WGS AF: 0.00491 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9979250; hg19: chr21-40283733;