rs10504249

Variant names:

• chr8-57876522-A-G
• rs10504249
• ENST00000650579.1:n.326+11904A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-57876522-A-G
• chr8-57876522-A-T

Variant summary

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

The ENST00000650579.1(LINC01602):​n.326+11904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 152,316 control chromosomes in the GnomAD database, including 100 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 0.018 (100 hom., cov: 32)
• Consequence: LINC01602 ENST00000650579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 3 publications found

Genes affected

LINC01602 (HGNC:51634): (long intergenic non-protein coding RNA 1602)

LOC105375856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375856	XR_928921.2	n.348+11904A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01602	ENST00000650579.1	n.326+11904A>G		intron_variant	Intron 2 of 3
LINC01602	ENST00000805089.1	n.374+11904A>G		intron_variant	Intron 2 of 2
LINC01602	ENST00000805090.1	n.375-5254A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2673 AN: 152198 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.00379

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.00455

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0176 AC: 2686 AN: 152316 Hom.: 100 Cov.: 32 AF XY: 0.0182 AC XY: 1358 AN XY: 74488

African (AFR) AF: 0.00378 AC: 157 AN: 41580

American (AMR) AF: 0.0926 AC: 1416 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.00456 AC: 22 AN: 4826

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 887 AN: 68026

Other (OTH) AF: 0.0170 AC: 36 AN: 2112

Alfa AF: 0.0161 Hom.: 20

Bravo AF: 0.0235

Asia WGS AF: 0.00924 AC: 32 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	0.72
DANN	Benign	0.68
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10504249; hg19: chr8-58789081;