rs2989476

chr1-60593587-G-C

Variant summary

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

The NR_146508.1(LINC01748):n.1149+1951C>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 0.472 in 151,974 control chromosomes in the GnomAD database, including 17,390 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 0.47 (17390 hom., cov: 32)
• Consequence: LINC01748 NR_146508.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LINC01748 (HGNC:52535): (long intergenic non-protein coding RNA 1748)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01748	NR_146508.1	n.1149+1951C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01748	ENST00000661790.1	n.1196+1951C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71673 AN: 151854 Hom.: 17366 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.472 AC: 71735 AN: 151974 Hom.: 17390 Cov.: 32 AF XY: 0.477 AC XY: 35399 AN XY: 74252

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.492

Alfa AF: 0.434 Hom.: 8168

Bravo AF: 0.489

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0090
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2989476; hg19: chr1-61059259;