10-123488934-T-C

Variant names:

• chr10-123488934-T-C
• rs1556852
• ENST00000448671.2:n.710T>C

Variant summary

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

The ENST00000448671.2(LINC02641):​n.710T>C 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 0.508 in 152,170 control chromosomes in the GnomAD database, including 20,636 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 (20628 hom., cov: 33)
  • Exomes 𝑓: 0.50 (8 hom.)
• Consequence: LINC02641 ENST00000448671.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1010T>C		non_coding_transcript_exon_variant	Exon 2 of 6
LINC02641	XR_001747617.3	n.289T>C		non_coding_transcript_exon_variant	Exon 3 of 7
LINC02641	XR_001747618.2	n.267T>C		non_coding_transcript_exon_variant	Exon 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448671.2	n.710T>C		non_coding_transcript_exon_variant	Exon 5 of 5	3
LINC02641	ENST00000655916.1	n.300T>C		non_coding_transcript_exon_variant	Exon 3 of 4
LINC02641	ENST00000663275.1	n.305T>C		non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77222 AN: 152002 Hom.: 20585 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.500 AC: 25 AN: 50 Hom.: 8 Cov.: 0 AF XY: 0.654 AC XY: 17 AN XY: 26

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.508 AC: 77321 AN: 152120 Hom.: 20628 Cov.: 33 AF XY: 0.504 AC XY: 37456 AN XY: 74350

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.488

Alfa AF: 0.323 Hom.: 788

Bravo AF: 0.533

Asia WGS AF: 0.425 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556852; hg19: chr10-125248450;