5-161931882-C-G

Variant names:

• chr5-161931882-C-G
• rs1350375
• ENST00000625268.2:n.418-8018G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625268.2(LINC01202):​n.418-8018G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,068 control chromosomes in the GnomAD database, including 48,535 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 0.79 (48535 hom., cov: 31)
• Consequence: LINC01202 ENST00000625268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

LINC01202 (HGNC:49633): (long intergenic non-protein coding RNA 1202)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625268.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01202	NR_126372.1		n.78-8018G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01202	ENST00000625268.2	TSL:3	n.418-8018G>C		intron	N/A
	LINC01202	ENST00000812067.1		n.182-21049G>C		intron	N/A
	LINC01202	ENST00000812068.1		n.395-21049G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120333 AN: 151952 Hom.: 48480 Cov.: 31

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.792 AC: 120444 AN: 152068 Hom.: 48535 Cov.: 31 AF XY: 0.789 AC XY: 58632 AN XY: 74298

African (AFR) AF: 0.942 AC: 39125 AN: 41546

American (AMR) AF: 0.783 AC: 11957 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3796 AN: 5154

South Asian (SAS) AF: 0.776 AC: 3729 AN: 4804

European-Finnish (FIN) AF: 0.656 AC: 6912 AN: 10538

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50171 AN: 67970

Other (OTH) AF: 0.760 AC: 1601 AN: 2106

Alfa AF: 0.772 Hom.: 5372

Bravo AF: 0.806

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1350375; hg19: chr5-161358888;