rs2473307

chr1-22024341-T-C

Variant summary

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

The NR_110692.1(LINC01635):n.351A>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 0.549 in 152,112 control chromosomes in the GnomAD database, including 23,703 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 0.55 (23696 hom., cov: 32)
  • Exomes 𝑓: 0.55 (7 hom.)
• Consequence: LINC01635 NR_110692.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

LINC01635 (HGNC:52422): (long intergenic non-protein coding RNA 1635)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01635	NR_110692.1	n.351A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01635	ENST00000455966.2	n.351A>G		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83339 AN: 151930 Hom.: 23660 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.568

GnomAD4 exome AF: 0.548 AC: 34 AN: 62 Hom.: 7 Cov.: 0 AF XY: 0.587 AC XY: 27 AN XY: 46

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.520

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.549 AC: 83428 AN: 152050 Hom.: 23696 Cov.: 32 AF XY: 0.542 AC XY: 40281 AN XY: 74312

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.572

Alfa AF: 0.526 Hom.: 4469

Bravo AF: 0.548

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2473307; hg19: chr1-22350834;