rs10996614

Variant names:

• chr10-65728784-T-C
• rs10996614
• ENST00000595269.5:n.236-8113T>C

Variant summary

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

The ENST00000595269.5(LINC01515):​n.236-8113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,054 control chromosomes in the GnomAD database, including 397 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 0.067 (397 hom., cov: 31)
• Consequence: LINC01515 ENST00000595269.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 3 publications found

Genes affected

LINC01515 (HGNC:51210): (long intergenic non-protein coding RNA 1515)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01515	NR_120647.1	n.513-8113T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01515	ENST00000595269.5	n.236-8113T>C		intron_variant	Intron 2 of 3	5
LINC01515	ENST00000626101.2	n.139-37772T>C		intron_variant	Intron 2 of 3	5
LINC01515	ENST00000626907.2	n.138+39173T>C		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0672 AC: 10210 AN: 151932 Hom.: 398 Cov.: 31

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.0935

Gnomad NFE AF: 0.0532

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0673 AC: 10230 AN: 152054 Hom.: 397 Cov.: 31 AF XY: 0.0668 AC XY: 4965 AN XY: 74330

African (AFR) AF: 0.0940 AC: 3898 AN: 41462

American (AMR) AF: 0.0669 AC: 1020 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0612 AC: 212 AN: 3464

East Asian (EAS) AF: 0.0632 AC: 326 AN: 5156

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4822

European-Finnish (FIN) AF: 0.0450 AC: 477 AN: 10590

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0532 AC: 3619 AN: 67992

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0596 Hom.: 179

Bravo AF: 0.0713

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.4
DANN	Benign	0.93
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10996614; hg19: chr10-67488542;