ENST00000448347.5:n.587-40563A>C

Variant names:

• chr10-123408790-A-C
• rs6599695
• ENST00000448347.5:n.587-40563A>C

Variant summary

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

The ENST00000448347.5(LINC02641):​n.587-40563A>C variant causes a intron 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 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 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.587-40563A>C		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.539-40563A>C		intron	N/A
	LINC02641	ENST00000662754.1		n.337+47240A>C		intron	N/A

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

African (AFR) AF: 0.759 AC: 31519 AN: 41504

American (AMR) AF: 0.507 AC: 7757 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1289 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3315 AN: 5176

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4814

European-Finnish (FIN) AF: 0.306 AC: 3238 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27259 AN: 67982

Other (OTH) AF: 0.498 AC: 1053 AN: 2114

Alfa AF: 0.433 Hom.: 25175

Bravo AF: 0.539

Asia WGS AF: 0.503 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6599695;

hg19: chr10-125168306;