2-103964045-C-T

Variant names:

• chr2-103964045-C-T
• rs12613775
• ENST00000537492.5:n.137-89459C>T

Variant summary

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

The ENST00000537492.5(LINC01965):​n.137-89459C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,034 control chromosomes in the GnomAD database, including 2,515 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 0.17 (2515 hom., cov: 31)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01965	XR_001739621.2	n.158-89459C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01965	ENST00000537492.5	n.137-89459C>T		intron_variant	Intron 1 of 3	4
LINC01965	ENST00000544869.5	n.116-89459C>T		intron_variant	Intron 1 of 2	4
LINC01965	ENST00000688553.2	n.294-89459C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26322 AN: 151914 Hom.: 2509 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0980

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.173 AC: 26340 AN: 152034 Hom.: 2515 Cov.: 31 AF XY: 0.170 AC XY: 12643 AN XY: 74282

African (AFR) AF: 0.246 AC: 10211 AN: 41460

American (AMR) AF: 0.0945 AC: 1443 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1258 AN: 5152

South Asian (SAS) AF: 0.152 AC: 730 AN: 4818

European-Finnish (FIN) AF: 0.0980 AC: 1036 AN: 10570

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10533 AN: 67982

Other (OTH) AF: 0.147 AC: 310 AN: 2110

Alfa AF: 0.161 Hom.: 9085

Bravo AF: 0.175

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.71
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12613775; hg19: chr2-104580503;