rs11903187

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-103972680-G-A
• chr2-103972680-G-T

Variant summary

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

The ENST00000537492.5(LINC01965):​n.137-80824G>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01965	XR_001739621.2	n.158-80824G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01965	ENST00000537492.5	n.137-80824G>A		intron_variant	Intron 1 of 3	4
LINC01965	ENST00000544869.5	n.116-80824G>A		intron_variant	Intron 1 of 2	4
LINC01965	ENST00000688553.2	n.294-80824G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs11903187; hg19: chr2-104589138;