ENST00000537492.5:n.137-80824G>A

Variant names:

• chr2-103972680-G-A
• rs11903187
• ENST00000537492.5:n.137-80824G>A

Variant summary

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

The ENST00000537492.5(LINC01965):​n.137-80824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,050 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 3 publications found

Genes affected

LINC01965 (HGNC:52790): (long intergenic non-protein coding RNA 1965)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537492.5. 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
	LINC01965	ENST00000537492.5	TSL:4	n.137-80824G>A		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.116-80824G>A		intron	N/A
	LINC01965	ENST00000688553.2		n.294-80824G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26900 AN: 151930 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.177 AC: 26920 AN: 152050 Hom.: 2640 Cov.: 32 AF XY: 0.174 AC XY: 12925 AN XY: 74344

African (AFR) AF: 0.258 AC: 10700 AN: 41442

American (AMR) AF: 0.0968 AC: 1479 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5160

South Asian (SAS) AF: 0.151 AC: 729 AN: 4822

European-Finnish (FIN) AF: 0.0982 AC: 1041 AN: 10596

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10587 AN: 67974

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.171 Hom.: 3364

Bravo AF: 0.180

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.46
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism

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: rs11903187;

hg19: chr2-104589138;