rs9979250

Variant names:

• chr21-38911809-C-T
• rs9979250
• ENST00000776941.1:n.48C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000776941.1(ENSG00000301200):​n.48C>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 0.03 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: ENSG00000301200 ENST00000776941.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

Genes affected

ENSG00000301200 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 112 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1	n.677-9844G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301200	ENST00000776941.1	n.48C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ETS2-AS1	ENST00000380931.6	n.677-9844G>A		intron_variant	Intron 2 of 3	2
ETS2-AS1	ENST00000415824.1	n.277-9844G>A		intron_variant	Intron 2 of 3	5

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

African (AFR) AF: 0.00832 AC: 346 AN: 41576

American (AMR) AF: 0.0254 AC: 389 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0869 AC: 301 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4824

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3150 AN: 68030

Other (OTH) AF: 0.0241 AC: 51 AN: 2116

Alfa AF: 0.0410 Hom.: 177

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
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9979250; hg19: chr21-40283733;