rs4881171

Positions:

• chr10-3450696-G-A
• chr10-3450696-G-C

Variant summary

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

The XR_007062362.1(LOC124902538):​n.1063G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,982 control chromosomes in the GnomAD database, including 2,270 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 0.15 (2270 hom., cov: 32)
• Consequence: LOC124902538 XR_007062362.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

LOC124902538 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902538	XR_007062362.1	n.1063G>A		non_coding_transcript_exon_variant	1/2
LOC105376360	NR_131187.1	n.162+131840G>A		intron_variant, non_coding_transcript_variant
LINC02669	NR_155743.1	n.632-15718C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000660786.1	n.645-15718C>T		intron_variant, non_coding_transcript_variant
LINC02669	ENST00000659295.1	n.482-15718C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23201 AN: 151864 Hom.: 2267 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.153 AC: 23218 AN: 151982 Hom.: 2270 Cov.: 32 AF XY: 0.160 AC XY: 11920 AN XY: 74286

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0835

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.0982

Gnomad4 OTH AF: 0.135

Alfa AF: 0.120 Hom.: 189

Bravo AF: 0.159

Asia WGS AF: 0.275 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4881171; hg19: chr10-3492888;