rs10514310

Variant names:

• chr5-89725761-A-G
• rs10514310
• XR_948556.3:n.161-43494A>G

Variant summary

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

The XR_948556.3(LINC02161):​n.161-43494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 151,400 control chromosomes in the GnomAD database, including 844 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 0.096 (844 hom., cov: 32)
• Consequence: LINC02161 XR_948556.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 3 publications found

Genes affected

LINC02161 (HGNC:53022): (long intergenic non-protein coding RNA 2161)

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 (AMR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0958 AC: 14487 AN: 151280 Hom.: 845 Cov.: 32

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.0957 AC: 14490 AN: 151400 Hom.: 844 Cov.: 32 AF XY: 0.0969 AC XY: 7165 AN XY: 73974

African (AFR) AF: 0.0534 AC: 2213 AN: 41422

American (AMR) AF: 0.164 AC: 2480 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 562 AN: 3430

East Asian (EAS) AF: 0.147 AC: 752 AN: 5126

South Asian (SAS) AF: 0.0834 AC: 402 AN: 4820

European-Finnish (FIN) AF: 0.0706 AC: 750 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6923 AN: 67526

Other (OTH) AF: 0.118 AC: 248 AN: 2098

Alfa AF: 0.104 Hom.: 1516

Bravo AF: 0.103

Asia WGS AF: 0.129 AC: 448 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	0.70
DANN	Benign	0.66
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10514310; hg19: chr5-89021578;