rs10504741

chr8-81843118-C-Achr8-81843118-C-Gchr8-81843118-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_170318.1(LINC02235):n.272+228C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,088 control chromosomes in the GnomAD database, including 27,746 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 0.60 (27746 hom., cov: 33)
• Consequence: LINC02235 NR_170318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

LINC02235 (HGNC:53106): (long intergenic non-protein coding RNA 2235)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02235	NR_170318.1	n.272+228C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02235	ENST00000670794.1	n.151+1016C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90610 AN: 151970 Hom.: 27733 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.596 AC: 90661 AN: 152088 Hom.: 27746 Cov.: 33 AF XY: 0.604 AC XY: 44899 AN XY: 74340

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.588

Alfa AF: 0.575 Hom.: 3711

Bravo AF: 0.592

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.5
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504741; hg19: chr8-82755353;