rs113808744

Variant names:

• chr10-69989919-T-C
• rs113808744
• NR_184064.1:n.5753A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_184064.1(LINC02636):​n.5753A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 152,316 control chromosomes in the GnomAD database, including 38 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 0.015 (38 hom., cov: 33)
• Consequence: LINC02636 NR_184064.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

Genes affected

LINC02636 (HGNC:54119): (long intergenic non-protein coding RNA 2636)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0149 (2265/152316) while in subpopulation AFR AF = 0.0393 (1632/41570). AF 95% confidence interval is 0.0377. There are 38 homozygotes in GnomAd4. There are 1073 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02636	NR_184064.1	n.5753A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LINC02636	NR_184065.1	n.5865A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02636	NR_184066.1	n.5861A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0149 AC: 2261 AN: 152198 Hom.: 38 Cov.: 33

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00936

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00433

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00509

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0149 AC: 2265 AN: 152316 Hom.: 38 Cov.: 33 AF XY: 0.0144 AC XY: 1073 AN XY: 74482

African (AFR) AF: 0.0393 AC: 1632 AN: 41570

American (AMR) AF: 0.00935 AC: 143 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4820

European-Finnish (FIN) AF: 0.00433 AC: 46 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00509 AC: 346 AN: 68026

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.0101 Hom.: 8

Bravo AF: 0.0169

Asia WGS AF: 0.00347 AC: 12 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.7
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs113808744; hg19: chr10-71749675;