rs2165468

Positions:

• chr10-3473913-C-A

Variant summary

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

The NR_131187.1(LOC105376360):​n.162+155057C>A 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 0.201 in 152,024 control chromosomes in the GnomAD database, including 3,748 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 0.20 (3748 hom., cov: 32)
• Consequence: LOC105376360 NR_131187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

LINC02669 (HGNC:54155): (long intergenic non-protein coding RNA 2669)

LOC105376360 (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 (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+155057C>A		intron_variant, non_coding_transcript_variant
LINC02669	NR_155743.1	n.631+23740G>T		intron_variant, non_coding_transcript_variant
LOC124902538	XR_007062362.1	n.3056+21224C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000660786.1	n.644+23740G>T		intron_variant, non_coding_transcript_variant
LINC02669	ENST00000659295.1	n.481+23740G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30491 AN: 151906 Hom.: 3747 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.201 AC: 30505 AN: 152024 Hom.: 3748 Cov.: 32 AF XY: 0.210 AC XY: 15572 AN XY: 74286

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.179

Alfa AF: 0.145 Hom.: 2478

Bravo AF: 0.208

Asia WGS AF: 0.272 AC: 943 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	0.55
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165468; hg19: chr10-3516105;