rs448013

Positions:

• chr20-55682857-G-A

Variant summary

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

The ENST00000661549.1(ENSG00000287478):​n.30-15231C>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 0.0574 in 152,104 control chromosomes in the GnomAD database, including 503 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 0.057 (503 hom., cov: 32)
• Consequence: ENST00000661549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.51

Genes affected

(HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984001	XR_007067757.1	n.236-15231C>T		intron_variant, non_coding_transcript_variant
LOC107984001	XR_936884.3	n.236-15231C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661549.1	n.30-15231C>T		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000667361.1	n.1634-1766G>A		intron_variant, non_coding_transcript_variant
LINC01440	ENST00000664886.1	n.832-1766G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8725 AN: 151986 Hom.: 505 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0574 AC: 8729 AN: 152104 Hom.: 503 Cov.: 32 AF XY: 0.0603 AC XY: 4483 AN XY: 74356

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.0628

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.0713

Gnomad4 FIN AF: 0.0339

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0602

Alfa AF: 0.0351 Hom.: 78

Bravo AF: 0.0635

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.031
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs448013; hg19: chr20-54257915; COSMIC: COSV62508882;