rs11903187

chr2-103972680-G-Achr2-103972680-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688553.1(LINC01965):n.211-80824G>A variant causes a intron, non coding transcript 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 ENST00000688553.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01965	XR_001739621.2	n.158-80824G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01965	ENST00000688553.1	n.211-80824G>A		intron_variant, non_coding_transcript_variant
LINC01965	ENST00000537492.5	n.137-80824G>A		intron_variant, non_coding_transcript_variant		4
LINC01965	ENST00000544869.5	n.116-80824G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0968

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.149

Alfa AF: 0.173 Hom.: 318

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11903187; hg19: chr2-104589138;