rs1902356

Variant names:

• chr10-65674275-G-A
• rs1902356
• ENST00000433152.8:n.833-6685G>A

Variant summary

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

The NR_120647.1(LINC01515):​n.404-15228G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 151,976 control chromosomes in the GnomAD database, including 105 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 0.031 (105 hom., cov: 32)
• Consequence: LINC01515 NR_120647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 0 publications found

Genes affected

LINC01515 (HGNC:51210): (long intergenic non-protein coding RNA 1515)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120647.1. 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
	LINC01515	NR_120647.1		n.404-15228G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01515	ENST00000433152.8	TSL:5	n.833-6685G>A		intron	N/A
	LINC01515	ENST00000594054.5	TSL:5	n.26-7915G>A		intron	N/A
	LINC01515	ENST00000595269.5	TSL:5	n.127-15228G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4637 AN: 151858 Hom.: 103 Cov.: 32

Gnomad AFR AF: 0.00712

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0305 AC: 4636 AN: 151976 Hom.: 105 Cov.: 32 AF XY: 0.0322 AC XY: 2392 AN XY: 74280

African (AFR) AF: 0.00712 AC: 295 AN: 41434

American (AMR) AF: 0.0523 AC: 798 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3468

East Asian (EAS) AF: 0.130 AC: 672 AN: 5164

South Asian (SAS) AF: 0.0339 AC: 163 AN: 4806

European-Finnish (FIN) AF: 0.0317 AC: 335 AN: 10570

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0322 AC: 2190 AN: 67970

Other (OTH) AF: 0.0242 AC: 51 AN: 2108

Alfa AF: 0.0292 Hom.: 8

Bravo AF: 0.0312

Asia WGS AF: 0.0810 AC: 280 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.43
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs1902356; hg19: chr10-67434033;