1-148354530-T-G

Variant names:

• chr1-148354530-T-G
• rs2932454
• ENST00000762844.1:n.415T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762844.1(ENSG00000299363):​n.415T>G variant causes a non coding transcript exon 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: ENSG00000299363 ENST00000762844.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 4 publications found

Genes affected

ENSG00000299363 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299363	ENST00000762844.1	n.415T>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000299363	ENST00000762845.1	n.161T>G		non_coding_transcript_exon_variant	Exon 2 of 3
LINC01138	ENST00000638958.1	n.233-20417A>C		intron_variant	Intron 1 of 6	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

African (AFR) AF: 0.358 AC: 14836 AN: 41404

American (AMR) AF: 0.202 AC: 3086 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1073 AN: 5152

South Asian (SAS) AF: 0.141 AC: 679 AN: 4814

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10546

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10161 AN: 67966

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.152 Hom.: 1200

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2932454; hg19: chr1-147826658;