14-41034020-C-A

Variant names:

• chr14-41034020-C-A
• rs2211549
• ENST00000651006.2:n.642+59630C>A

Variant summary

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

The ENST00000651006.2(LINC02315):​n.642+59630C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,066 control chromosomes in the GnomAD database, including 1,721 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 0.10 (1721 hom., cov: 33)
• Consequence: LINC02315 ENST00000651006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 0 publications found

Genes affected

LINC02315 (HGNC:53234): (long intergenic non-protein coding RNA 2315)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02315	NR_109758.1	n.346+59630C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02315	ENST00000651006.2	n.642+59630C>A		intron_variant	Intron 3 of 3
LINC02315	ENST00000719278.1	n.386+59630C>A		intron_variant	Intron 4 of 4
LINC02315	ENST00000719279.1	n.449+59630C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15264 AN: 151948 Hom.: 1717 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0940

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.00699

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.101 AC: 15291 AN: 152066 Hom.: 1721 Cov.: 33 AF XY: 0.100 AC XY: 7435 AN XY: 74320

African (AFR) AF: 0.270 AC: 11201 AN: 41434

American (AMR) AF: 0.0595 AC: 909 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0940 AC: 326 AN: 3468

East Asian (EAS) AF: 0.137 AC: 707 AN: 5164

South Asian (SAS) AF: 0.113 AC: 544 AN: 4816

European-Finnish (FIN) AF: 0.00699 AC: 74 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0194 AC: 1320 AN: 68008

Other (OTH) AF: 0.0883 AC: 186 AN: 2106

Alfa AF: 0.00378 Hom.: 1

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 547 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.32
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs2211549; hg19: chr14-41503225;