chr10-123490466-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448347.5. 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	ENST00000448347.5	TSL:3	n.747-27158C>T		intron	N/A
	LINC02641	ENST00000655916.1		n.376+1456C>T		intron	N/A
	LINC02641	ENST00000662754.1		n.338-33386C>T		intron	N/A

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 v4.9

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;