rs7729084

Positions:

• chr5-174954577-A-C
• chr5-174954577-A-T

Variant summary

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

The NR_046113.1(LINC01951):​n.1499+21872T>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 0.224 in 152,176 control chromosomes in the GnomAD database, including 9,455 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 (9455 hom., cov: 33)
• Consequence: LINC01951 NR_046113.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

LINC01951 (HGNC:52774): (long intergenic non-protein coding RNA 1951)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01951	NR_046113.1	n.1499+21872T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01951	ENST00000377300.3	n.1281+21872T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33900 AN: 152058 Hom.: 9400 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.224 AC: 34017 AN: 152176 Hom.: 9455 Cov.: 33 AF XY: 0.216 AC XY: 16039 AN XY: 74410

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.192

Alfa AF: 0.0660 Hom.: 556

Bravo AF: 0.249

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.057
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7729084; hg19: chr5-174381580;