rs11696973

chr20-55551451-G-T

Variant summary

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

The ENST00000667361.1(LINC01440):n.1480+83237G>T 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 0.128 in 152,162 control chromosomes in the GnomAD database, including 1,305 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 (1305 hom., cov: 32)
• Consequence: LINC01440 ENST00000667361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

LINC01440 (HGNC:50762): (long intergenic non-protein coding RNA 1440)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01440	ENST00000667361.1	n.1480+83237G>T		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000654685.1	n.918-9378G>T		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000664886.1	n.648+83237G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19427 AN: 152044 Hom.: 1304 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.128 AC: 19444 AN: 152162 Hom.: 1305 Cov.: 32 AF XY: 0.124 AC XY: 9206 AN XY: 74416

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.123

Alfa AF: 0.135 Hom.: 173

Bravo AF: 0.129

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.4
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696973; hg19: chr20-54126509;