chr10-123466662-C-A

Position:

• chr10-123466662-C-A

Variant summary

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

The ENST00000662754.1(LINC02641):​n.338-57190C>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 0.296 in 152,106 control chromosomes in the GnomAD database, including 7,658 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 0.30 (7658 hom., cov: 33)
• Consequence: LINC02641 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02641	XR_007062326.1	n.9069+17150C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000662754.1	n.338-57190C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45013 AN: 151988 Hom.: 7647 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.296 AC: 45039 AN: 152106 Hom.: 7658 Cov.: 33 AF XY: 0.302 AC XY: 22467 AN XY: 74344

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.328

Alfa AF: 0.348 Hom.: 16216

Bravo AF: 0.280

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.030
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs705145; hg19: chr10-125226178;