rs705670

Positions:

• chr9-135576738-C-G
• chr9-135576738-C-T

Variant summary

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

The NR_034016.1(LINC01502):​n.171-612C>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 0.358 in 152,148 control chromosomes in the GnomAD database, including 10,310 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 0.36 (10310 hom., cov: 33)
• Consequence: LINC01502 NR_034016.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

LINC01502 (HGNC:51183): (long intergenic non-protein coding RNA 1502)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01502	NR_034016.1	n.171-612C>G		intron_variant, non_coding_transcript_variant
LINC01502	NR_034017.1	n.171-612C>G		intron_variant, non_coding_transcript_variant
LINC01502	NR_109814.1	n.171-612C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01502	ENST00000445997.1	n.145-612C>G		intron_variant, non_coding_transcript_variant		2
LINC01502	ENST00000447907.5	n.161-612C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54415 AN: 152030 Hom.: 10295 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.358 AC: 54464 AN: 152148 Hom.: 10310 Cov.: 33 AF XY: 0.360 AC XY: 26753 AN XY: 74356

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.358

Alfa AF: 0.326 Hom.: 1034

Bravo AF: 0.375

Asia WGS AF: 0.480 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs705670; hg19: chr9-138468584;