rs6599695

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_002957104.1	n.6363-40563A>C		intron_variant	Intron 4 of 9
LINC02641	XR_002957105.1	n.5694-40563A>C		intron_variant	Intron 3 of 8
LINC02641	XR_007062326.1	n.8910-40563A>C		intron_variant	Intron 6 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.587-40563A>C		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000448671.2	n.539-40563A>C		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000662754.1	n.337+47240A>C		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs6599695; hg19: chr10-125168306;