rs10495827

Variant names:

• chr2-34723336-C-T
• rs10495827
• ENST00000659537.2:n.1890C>T

Variant summary

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

The ENST00000659537.2(LINC01320):​n.1890C>T 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 0.212 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: LINC01320 ENST00000659537.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 1 publications found

Genes affected

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

LOC105374458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105374458	XR_002959378.2	n.607+5825G>A		intron_variant	Intron 3 of 5
LOC105374458	XR_007086277.1	n.571+5825G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000659537.2	n.1890C>T		non_coding_transcript_exon_variant	Exon 6 of 6
LINC01320	ENST00000453774.2	n.351-9112C>T		intron_variant	Intron 3 of 4	3
LINC01320	ENST00000603129.6	n.307+1215C>T		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.122 AC: 5059 AN: 41488

American (AMR) AF: 0.190 AC: 2902 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3468

East Asian (EAS) AF: 0.0298 AC: 154 AN: 5170

South Asian (SAS) AF: 0.148 AC: 715 AN: 4824

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19110 AN: 67992

Other (OTH) AF: 0.241 AC: 508 AN: 2110

Alfa AF: 0.231 Hom.: 693

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
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs10495827; hg19: chr2-34948403;