2-176817054-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000230552 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC01117	ENST00000814417.1	n.72A>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000230552	ENST00000451851.1	n.74+2183T>C		intron_variant	Intron 1 of 5	4

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

African (AFR) AF: 0.855 AC: 35362 AN: 41366

American (AMR) AF: 0.985 AC: 15055 AN: 15288

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 1.00 AC: 4814 AN: 4814

European-Finnish (FIN) AF: 1.00 AC: 10609 AN: 10610

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67954 AN: 68006

Other (OTH) AF: 0.964 AC: 2037 AN: 2112

Alfa AF: 0.983 Hom.: 68867

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
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs840689; hg19: chr2-177681782;