rs10514310

chr5-89725761-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948556.3(LINC02161):n.161-43494A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

Genes affected

LINC02161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02161	XR_948556.3	n.161-43494A>G		intron_variant, non_coding_transcript_variant
LINC02161	XR_948557.3	n.70+39693A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.118

Alfa AF: 0.108 Hom.: 1024

Bravo AF: 0.103

Asia WGS AF: 0.129 AC: 448 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	0.70
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514310; hg19: chr5-89021578;