rs705145

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-123466662-C-A
• chr10-123466662-C-G
• chr10-123466662-C-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
• Publications: 10 publications found

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812864.1. 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
	ENSG00000305771	ENST00000812864.1		n.512G>T		non_coding_transcript_exon	Exon 2 of 2
	LINC02641	ENST00000448347.5	TSL:3	n.746+17150C>A		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.698+17150C>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs705145;

hg19: chr10-125226178;