10-123466662-C-A

Variant names:

• chr10-123466662-C-A
• rs705145
• ENST00000812864.1:n.512G>T

Variant summary

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

The ENST00000812864.1(ENSG00000305771):​n.512G>T 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 0.296 in 152,106 control chromosomes in the GnomAD database, including 7,658 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 0.30 (7658 hom., cov: 33)
• Consequence: ENSG00000305771 ENST00000812864.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

ENSG00000305771 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747617.3	n.277+17150C>A		intron_variant	Intron 2 of 6
LINC02641	XR_001747619.3	n.118-22261C>A		intron_variant	Intron 1 of 5
LINC02641	XR_002957104.1	n.6522+17150C>A		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305771	ENST00000812864.1	n.512G>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02641	ENST00000448347.5	n.746+17150C>A		intron_variant	Intron 4 of 4	3
LINC02641	ENST00000448671.2	n.698+17150C>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45013 AN: 151988 Hom.: 7647 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.296 AC: 45039 AN: 152106 Hom.: 7658 Cov.: 33 AF XY: 0.302 AC XY: 22467 AN XY: 74344

African (AFR) AF: 0.126 AC: 5246 AN: 41530

American (AMR) AF: 0.302 AC: 4612 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2200 AN: 5176

South Asian (SAS) AF: 0.491 AC: 2362 AN: 4812

European-Finnish (FIN) AF: 0.353 AC: 3727 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24277 AN: 67966

Other (OTH) AF: 0.328 AC: 692 AN: 2110

Alfa AF: 0.338 Hom.: 36967

Bravo AF: 0.280

Asia WGS AF: 0.467 AC: 1624 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	0.030
DANN	Benign	0.46
PhyloP100		-2.8

Splicing

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

Publications

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Other links and lift over

dbSNP: rs705145; hg19: chr10-125226178;