rs10495620

Variant names:

• chr2-13976866-A-G
• rs10495620
• ENST00000417751.5:n.257-135252T>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.257-135252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,132 control chromosomes in the GnomAD database, including 10,512 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 0.26 (10512 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

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 (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.257-135252T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38968 AN: 152014 Hom.: 10481 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.257 AC: 39058 AN: 152132 Hom.: 10512 Cov.: 32 AF XY: 0.254 AC XY: 18916 AN XY: 74370

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.217

Alfa AF: 0.100 Hom.: 4292

Bravo AF: 0.278

Asia WGS AF: 0.302 AC: 1048 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	0.18
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495620; hg19: chr2-14116991;