1-148353534-T-C

Variant names:

• chr1-148353534-T-C
• rs2999617
• ENST00000760740.1:n.787A>G

Variant summary

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

The ENST00000760740.1(LINC01138):​n.787A>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 0.219 in 151,848 control chromosomes in the GnomAD database, including 4,435 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 (4435 hom., cov: 31)
• Consequence: LINC01138 ENST00000760740.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 9 publications found

Genes affected

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

ENSG00000299363 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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
LINC01138	ENST00000760740.1	n.787A>G		non_coding_transcript_exon_variant	Exon 3 of 4
LINC01138	ENST00000638958.1	n.233-19421A>G		intron_variant	Intron 1 of 6	5
LINC01138	ENST00000640832.1	n.359-9153A>G		intron_variant	Intron 1 of 8	5

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33172 AN: 151730 Hom.: 4412 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.219 AC: 33244 AN: 151848 Hom.: 4435 Cov.: 31 AF XY: 0.218 AC XY: 16194 AN XY: 74184

African (AFR) AF: 0.379 AC: 15667 AN: 41358

American (AMR) AF: 0.200 AC: 3056 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1065 AN: 5144

South Asian (SAS) AF: 0.141 AC: 678 AN: 4806

European-Finnish (FIN) AF: 0.198 AC: 2090 AN: 10548

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9939 AN: 67958

Other (OTH) AF: 0.180 AC: 379 AN: 2108

Alfa AF: 0.165 Hom.: 7501

Bravo AF: 0.224

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2999617; hg19: chr1-147825662;