rs705162

Variant names:

• chr10-123492159-G-A
• rs705162
• ENST00000448347.5:n.747-25465G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-123492159-G-A
• chr10-123492159-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000448347.5(LINC02641):​n.747-25465G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,122 control chromosomes in the GnomAD database, including 4,323 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 0.21 (4323 hom., cov: 33)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 11 publications found

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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.747-25465G>A		intron	N/A
	LINC02641	ENST00000655916.1		n.376+3149G>A		intron	N/A
	LINC02641	ENST00000662754.1		n.338-31693G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32056 AN: 152004 Hom.: 4322 Cov.: 33

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.211 AC: 32072 AN: 152122 Hom.: 4323 Cov.: 33 AF XY: 0.215 AC XY: 16014 AN XY: 74358

African (AFR) AF: 0.0490 AC: 2035 AN: 41528

American (AMR) AF: 0.244 AC: 3725 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2043 AN: 5156

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4816

European-Finnish (FIN) AF: 0.223 AC: 2355 AN: 10582

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18077 AN: 67966

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.250 Hom.: 16562

Bravo AF: 0.202

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.87
PhyloP100		0.17

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: rs705162;

hg19: chr10-125251675;