rs6069325

chr20-55564428-T-G

Variant summary

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

The ENST00000667361.1(LINC01440):n.1480+96214T>G 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 0.141 in 151,090 control chromosomes in the GnomAD database, including 1,578 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 0.14 (1578 hom., cov: 30)
• Consequence: LINC01440 ENST00000667361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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+96214T>G		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000654685.1	n.1000+3517T>G		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000664886.1	n.648+96214T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21287 AN: 150976 Hom.: 1575 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.141 AC: 21307 AN: 151090 Hom.: 1578 Cov.: 30 AF XY: 0.137 AC XY: 10104 AN XY: 73800

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.136

Alfa AF: 0.155 Hom.: 221

Bravo AF: 0.141

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.76
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6069325; hg19: chr20-54139486;