rs705670

Variant names:

• chr9-135576738-C-G
• rs705670
• ENST00000445997.1:n.145-612C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445997.1(LINC01502):​n.145-612C>G variant causes a intron 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 ENST00000445997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445997.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01502	NR_034016.1		n.171-612C>G		intron	N/A
	LINC01502	NR_034017.1		n.171-612C>G		intron	N/A
	LINC01502	NR_109814.1		n.171-612C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01502	ENST00000445997.1	TSL:2	n.145-612C>G		intron	N/A
	LINC01502	ENST00000447907.5	TSL:3	n.161-612C>G		intron	N/A

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

African (AFR) AF: 0.449 AC: 18633 AN: 41500

American (AMR) AF: 0.393 AC: 6018 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.648 AC: 3339 AN: 5156

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4818

European-Finnish (FIN) AF: 0.287 AC: 3034 AN: 10588

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19430 AN: 68002

Other (OTH) AF: 0.358 AC: 756 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs705670;

hg19: chr9-138468584;