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
• Publications: 0 publications found

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417751.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00276	ENST00000417751.5	TSL:2	n.308-36394T>G		intron	N/A
	LINC00276	ENST00000747982.1		n.52-64957T>G		intron	N/A

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

African (AFR) AF: 0.135 AC: 5602 AN: 41518

American (AMR) AF: 0.537 AC: 8200 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1432 AN: 5166

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5547 AN: 10524

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39698 AN: 67932

Other (OTH) AF: 0.465 AC: 977 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.62
PhyloP100		-0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10495630;

hg19: chr2-13915803;