10-123408790-A-C

Position:

• chr10-123408790-A-C

Variant summary

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

The ENST00000662754.1(LINC02641):​n.337+47240A>C 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 0.512 in 152,144 control chromosomes in the GnomAD database, including 22,193 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 0.51 (22193 hom., cov: 33)
• Consequence: LINC02641 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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 (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02641	XR_007062326.1	n.8910-40563A>C		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957104.1	n.6363-40563A>C		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957105.1	n.5694-40563A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000662754.1	n.337+47240A>C		intron_variant, non_coding_transcript_variant
LINC02641	ENST00000448347.5	n.587-40563A>C		intron_variant, non_coding_transcript_variant		3
LINC02641	ENST00000448671.2	n.539-40563A>C		intron_variant, non_coding_transcript_variant		3
LINC02641	ENST00000671662.1	n.824+46643A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77848 AN: 152026 Hom.: 22161 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.512 AC: 77931 AN: 152144 Hom.: 22193 Cov.: 33 AF XY: 0.505 AC XY: 37564 AN XY: 74376

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.498

Alfa AF: 0.421 Hom.: 18486

Bravo AF: 0.539

Asia WGS AF: 0.503 AC: 1746 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	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6599695; hg19: chr10-125168306;