2-176817054-A-G

Variant names:

• chr2-176817054-A-G
• rs840689
• ENST00000428283.5:n.14+2183T>C

Variant summary

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

The ENST00000428283.5(ENSG00000230552):​n.14+2183T>C variant causes a intron change. The variant allele was found at a frequency of 0.958 in 152,036 control chromosomes in the GnomAD database, including 70,082 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 0.96 (70082 hom., cov: 30)
• Consequence: ENSG00000230552 ENST00000428283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.13

Genes affected

ENSG00000230552 (HGNC:):

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000230552	ENST00000428283.5	n.14+2183T>C		intron_variant	Intron 1 of 5	1
ENSG00000230552	ENST00000451851.1	n.74+2183T>C		intron_variant	Intron 1 of 5	4
LINC01117	ENST00000652227.1	n.640-1642A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145581 AN: 151920 Hom.: 70051 Cov.: 30

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.958 AC: 145665 AN: 152036 Hom.: 70082 Cov.: 30 AF XY: 0.958 AC XY: 71211 AN XY: 74324

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.985

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.964

Alfa AF: 0.991 Hom.: 50923

Bravo AF: 0.951

Asia WGS AF: 0.987 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840689; hg19: chr2-177681782;