1-148354530-T-G

Variant summary

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

The ENST00000640832.1(LINC01138):n.359-10149A>C 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 0.217 in 151,950 control chromosomes in the GnomAD database, including 4,271 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 0.22 (4271 hom., cov: 32)
• Consequence: LINC01138 ENST00000640832.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

LINC01138 (HGNC:49454): (long intergenic non-protein coding RNA 1138)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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
LINC01138	ENST00000640832.1	n.359-10149A>C		intron_variant, non_coding_transcript_variant		5
LINC01138	ENST00000638958.1	n.233-20417A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32884 AN: 151832 Hom.: 4252 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.217 AC: 32945 AN: 151950 Hom.: 4271 Cov.: 32 AF XY: 0.217 AC XY: 16104 AN XY: 74258

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.179

Alfa AF: 0.152 Hom.: 1124

Bravo AF: 0.220

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	2.5
Dann	Benign	0.046

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2932454; hg19: chr1-147826658;