rs1036736

Variant names:

• chr2-103962075-T-C
• rs1036736
• ENST00000537492.5:n.136+87630T>C

Variant summary

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

The ENST00000537492.5(LINC01965):​n.136+87630T>C 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 152,126 control chromosomes in the GnomAD database, including 2,604 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 (2604 hom., cov: 32)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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+87630T>C		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.115+87630T>C		intron	N/A
	LINC01965	ENST00000688553.2		n.293+87630T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26893 AN: 152008 Hom.: 2601 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0980

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.177 AC: 26908 AN: 152126 Hom.: 2604 Cov.: 32 AF XY: 0.174 AC XY: 12911 AN XY: 74350

African (AFR) AF: 0.252 AC: 10451 AN: 41478

American (AMR) AF: 0.100 AC: 1528 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1238 AN: 5142

South Asian (SAS) AF: 0.151 AC: 732 AN: 4832

European-Finnish (FIN) AF: 0.0980 AC: 1040 AN: 10608

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10685 AN: 68006

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.170 Hom.: 1148

Bravo AF: 0.180

Asia WGS AF: 0.141 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.49

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: rs1036736;

hg19: chr2-104578533;