10-123490466-C-T

Variant names:

• chr10-123490466-C-T
• rs1571423
• ENST00000448347.5:n.747-27158C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448347.5(LINC02641):​n.747-27158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,208 control chromosomes in the GnomAD database, including 4,123 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 0.23 (4123 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1086+1456C>T		intron_variant	Intron 2 of 5
LINC02641	XR_001747617.3	n.365+1456C>T		intron_variant	Intron 3 of 6
LINC02641	XR_001747618.2	n.343+1456C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.747-27158C>T		intron_variant	Intron 4 of 4	3
LINC02641	ENST00000655916.1	n.376+1456C>T		intron_variant	Intron 3 of 3
LINC02641	ENST00000662754.1	n.338-33386C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35028 AN: 152092 Hom.: 4125 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.230 AC: 35060 AN: 152208 Hom.: 4123 Cov.: 33 AF XY: 0.229 AC XY: 17059 AN XY: 74410

African (AFR) AF: 0.196 AC: 8153 AN: 41524

American (AMR) AF: 0.283 AC: 4332 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1609 AN: 5182

South Asian (SAS) AF: 0.181 AC: 872 AN: 4828

European-Finnish (FIN) AF: 0.213 AC: 2253 AN: 10600

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16404 AN: 67990

Other (OTH) AF: 0.253 AC: 533 AN: 2106

Alfa AF: 0.244 Hom.: 2399

Bravo AF: 0.239

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.54
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1571423; hg19: chr10-125249982;