17-50203294-GAA-GA

Variant names:

• chr17-50203294-GA-G
• rs11327935
• ENST00000509943.2:n.59+3361delA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000509943.2(ENSG00000249406):​n.59+3361delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 2,574 homozygotes. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.18 (2574 hom., cov: 28)
• Consequence: ENSG00000249406 ENST00000509943.2 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0550

Genes affected

ENSG00000249406 (HGNC:52795): (long intergenic non-protein coding RNA 1969)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249406	ENST00000509943.2	n.59+3361delA		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27336 AN: 151726 Hom.: 2572 Cov.: 28

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.180 AC: 27347 AN: 151846 Hom.: 2574 Cov.: 28 AF XY: 0.175 AC XY: 12951 AN XY: 74196

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.196

Alfa AF: 0.0595 Hom.: 77

Bravo AF: 0.181

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Bone mineral density variation quantitative trait locus Other:1

Aug 01, 2009

OMIM

Significance: association

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11327935; hg19: chr17-48280655;