chr17-50202995-G-C

Variant names:

• chr17-50202995-G-C
• rs2269336
• ENST00000509943.2:n.59+3061G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509943.2(ENSG00000249406):​n.59+3061G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,092 control chromosomes in the GnomAD database, including 3,189 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 0.19 (3189 hom., cov: 32)
• Consequence: ENSG00000249406 ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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+3061G>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29122 AN: 151974 Hom.: 3185 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.192 AC: 29166 AN: 152092 Hom.: 3189 Cov.: 32 AF XY: 0.196 AC XY: 14559 AN XY: 74350

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.202

Alfa AF: 0.0678 Hom.: 93

Bravo AF: 0.205

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
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: rs2269336; hg19: chr17-48280356;