rs1461356

Positions:

• chr1-60571343-G-A
• chr1-60571343-G-C
• chr1-60571343-G-T

Variant summary

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

The NR_146508.1(LINC01748):​n.1275+16694C>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 0.446 in 152,002 control chromosomes in the GnomAD database, including 15,519 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 0.45 (15519 hom., cov: 33)
• Consequence: LINC01748 NR_146508.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01748	NR_146508.1	n.1275+16694C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01748	ENST00000661790.1	n.1196+24195C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67718 AN: 151884 Hom.: 15502 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.446 AC: 67765 AN: 152002 Hom.: 15519 Cov.: 33 AF XY: 0.450 AC XY: 33465 AN XY: 74290

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.471

Alfa AF: 0.418 Hom.: 27851

Bravo AF: 0.460

Asia WGS AF: 0.628 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461356; hg19: chr1-61037015;