5-161931882-C-G

Position:

• chr5-161931882-C-G

Variant summary

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

The NR_126372.1(LINC01202):​n.78-8018G>C variant causes a intron, non coding transcript 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 NR_126372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01202	NR_126372.1	n.78-8018G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01202	ENST00000625268.2	n.418-8018G>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.760

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350375; hg19: chr5-161358888;