chr5-58244816-C-G

Variant names:

• chr5-58244816-C-G
• rs2964195
• ENST00000738711.1:n.122+14617G>C

Variant summary

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

The ENST00000738711.1(LINC02101):​n.122+14617G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,196 control chromosomes in the GnomAD database, including 68,639 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 0.95 (68639 hom., cov: 31)
• Consequence: LINC02101 ENST00000738711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 3 publications found

Genes affected

LINC02101 (HGNC:52956): (long intergenic non-protein coding RNA 2101)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738711.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02101	ENST00000738711.1		n.122+14617G>C		intron	N/A
	LINC02101	ENST00000738712.1		n.64+14617G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144368 AN: 152078 Hom.: 68585 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.949 AC: 144480 AN: 152196 Hom.: 68639 Cov.: 31 AF XY: 0.948 AC XY: 70482 AN XY: 74372

African (AFR) AF: 0.969 AC: 40227 AN: 41526

American (AMR) AF: 0.971 AC: 14854 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3319 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4867 AN: 5150

South Asian (SAS) AF: 0.923 AC: 4457 AN: 4830

European-Finnish (FIN) AF: 0.901 AC: 9536 AN: 10580

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64025 AN: 68026

Other (OTH) AF: 0.949 AC: 2007 AN: 2114

Alfa AF: 0.938 Hom.: 3120

Bravo AF: 0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.095
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2964195;

hg19: chr5-57540643;