chr2-103956547-C-T

Variant names:

• chr2-103956547-C-T
• rs2119507
• ENST00000537492.5:n.136+82102C>T

Variant summary

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

The ENST00000537492.5(LINC01965):​n.136+82102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,986 control chromosomes in the GnomAD database, including 1,399 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 0.13 (1399 hom., cov: 31)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• 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 (EAS) allele frequency at 95% confidence interval = 0.23 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.136+82102C>T		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.115+82102C>T		intron	N/A
	LINC01965	ENST00000655320.2		n.297-2747C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19980 AN: 151868 Hom.: 1398 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.132 AC: 19991 AN: 151986 Hom.: 1399 Cov.: 31 AF XY: 0.129 AC XY: 9601 AN XY: 74282

African (AFR) AF: 0.161 AC: 6680 AN: 41440

American (AMR) AF: 0.0736 AC: 1123 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1242 AN: 5142

South Asian (SAS) AF: 0.124 AC: 596 AN: 4808

European-Finnish (FIN) AF: 0.0791 AC: 835 AN: 10554

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8552 AN: 67996

Other (OTH) AF: 0.120 AC: 252 AN: 2106

Alfa AF: 0.128 Hom.: 2740

Bravo AF: 0.132

Asia WGS AF: 0.125 AC: 433 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	0.21
DANN	Benign	0.70
PhyloP100		-2.2

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: rs2119507;

hg19: chr2-104573005;