rs17043947

Positions:

• chr2-22514115-C-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.70+16921G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 151,916 control chromosomes in the GnomAD database, including 986 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 0.093 (986 hom., cov: 32)
• Consequence: ENSG00000228999 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

ENSG00000228999 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

LINC01884 (HGNC:52703): (long intergenic non-protein coding RNA 1884)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228999	ENST00000450551.1	n.70+16921G>A		intron_variant		5
LINC01884	ENST00000657386.1	n.50-2462C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14135 AN: 151798 Hom.: 976 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0933 AC: 14175 AN: 151916 Hom.: 986 Cov.: 32 AF XY: 0.0949 AC XY: 7044 AN XY: 74236

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0675

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0475 Hom.: 428

Bravo AF: 0.0960

Asia WGS AF: 0.135 AC: 471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17043947; hg19: chr2-22736987;