rs10495630

Variant names:

• chr2-13775678-A-C
• rs10495630
• ENST00000417751.5:n.308-36394T>G

Variant summary

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

The ENST00000417751.5(LINC00276):​n.308-36394T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,004 control chromosomes in the GnomAD database, including 17,060 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 0.43 (17060 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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.308-36394T>G		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65390 AN: 151886 Hom.: 17056 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.430 AC: 65404 AN: 152004 Hom.: 17060 Cov.: 32 AF XY: 0.428 AC XY: 31800 AN XY: 74284

Gnomad4 AFR AF: 0.135 AC: 0.134929 AN: 0.134929

Gnomad4 AMR AF: 0.537 AC: 0.53693 AN: 0.53693

Gnomad4 ASJ AF: 0.458 AC: 0.458213 AN: 0.458213

Gnomad4 EAS AF: 0.277 AC: 0.277197 AN: 0.277197

Gnomad4 SAS AF: 0.335 AC: 0.335133 AN: 0.335133

Gnomad4 FIN AF: 0.527 AC: 0.527081 AN: 0.527081

Gnomad4 NFE AF: 0.584 AC: 0.584378 AN: 0.584378

Gnomad4 OTH AF: 0.465 AC: 0.464795 AN: 0.464795

Alfa AF: 0.529 Hom.: 11364

Bravo AF: 0.422

Asia WGS AF: 0.300 AC: 1043 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495630; hg19: chr2-13915803;