10-123488934-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448671.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02641	ENST00000448671.2	TSL:3	n.710T>C		non_coding_transcript_exon	Exon 5 of 5
	LINC02641	ENST00000655916.1		n.300T>C		non_coding_transcript_exon	Exon 3 of 4
	LINC02641	ENST00000663275.1		n.305T>C		non_coding_transcript_exon	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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.545 AC: 24 AN: 44

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.670 AC: 27774 AN: 41474

American (AMR) AF: 0.564 AC: 8631 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2357 AN: 5170

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4812

European-Finnish (FIN) AF: 0.403 AC: 4266 AN: 10586

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29461 AN: 67996

Other (OTH) AF: 0.488 AC: 1032 AN: 2116

Alfa AF: 0.345 Hom.: 951

Bravo AF: 0.533

Asia WGS AF: 0.425 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.35
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1556852; hg19: chr10-125248450;