rs10495827

Positions:

• chr2-34723336-C-T

Variant summary

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

The XR_007086277.1(LOC105374458):​n.571+5825G>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 0.212 in 152,112 control chromosomes in the GnomAD database, including 3,891 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 (3891 hom., cov: 32)
• Consequence: LOC105374458 XR_007086277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

Genes affected

LOC105374458 (HGNC:):

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374458	XR_007086277.1	n.571+5825G>A		intron_variant, non_coding_transcript_variant
LOC105374458	XR_002959378.2	n.607+5825G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000659537.1	n.1456C>T		non_coding_transcript_exon_variant	2/2
LINC01320	ENST00000453774.2	n.351-9112C>T		intron_variant, non_coding_transcript_variant		3
LINC01320	ENST00000603129.6	n.307+1215C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32223 AN: 151994 Hom.: 3892 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.212 AC: 32225 AN: 152112 Hom.: 3891 Cov.: 32 AF XY: 0.207 AC XY: 15379 AN XY: 74348

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.241

Alfa AF: 0.235 Hom.: 690

Bravo AF: 0.206

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
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: rs10495827; hg19: chr2-34948403;