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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_001747616.2	n.1086+3149G>A		intron_variant	Intron 2 of 5
LINC02641	XR_001747617.3	n.365+3149G>A		intron_variant	Intron 3 of 6
LINC02641	XR_001747618.2	n.343+3149G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.747-25465G>A		intron_variant	Intron 4 of 4	3
LINC02641	ENST00000655916.1	n.376+3149G>A		intron_variant	Intron 3 of 3
LINC02641	ENST00000662754.1	n.338-31693G>A		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs705162; hg19: chr10-125251675;