rs11618266

Positions:

• chr13-77886223-A-G

Variant summary

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

The NR_103853.1(EDNRB-AS1):​n.1695-21469A>G 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 0.0223 in 152,176 control chromosomes in the GnomAD database, including 53 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 0.022 (53 hom., cov: 32)
• Consequence: EDNRB-AS1 NR_103853.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

EDNRB-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0223 (3396/152176) while in subpopulation NFE AF= 0.0352 (2390/67972). AF 95% confidence interval is 0.034. There are 53 homozygotes in gnomad4. There are 1589 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 53 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDNRB-AS1	NR_103853.1	n.1695-21469A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3396 AN: 152056 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00601

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00456

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0223 AC: 3396 AN: 152176 Hom.: 53 Cov.: 32 AF XY: 0.0214 AC XY: 1589 AN XY: 74388

Gnomad4 AFR AF: 0.00599

Gnomad4 AMR AF: 0.0158

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0302 Hom.: 29

Bravo AF: 0.0209

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11618266; hg19: chr13-78460358;