rs113808744

chr10-69989919-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02636 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02636	NR_184064.1	n.5753A>G		non_coding_transcript_exon_variant	4/4
LINC02636	NR_184065.1	n.5865A>G		non_coding_transcript_exon_variant	5/5
LINC02636	NR_184066.1	n.5861A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0393

Gnomad4 AMR AF: 0.00935

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00433

Gnomad4 NFE AF: 0.00509

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.0103 Hom.: 5

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113808744; hg19: chr10-71749675;