rs41386945

Variant names:

• chr14-41147028-C-T
• rs41386945
• ENST00000651006.2:n.643-2047C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651006.2(LINC02315):​n.643-2047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00453 in 143,352 control chromosomes in the GnomAD database, including 141 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 0.0045 (141 hom., cov: 28)
• Consequence: LINC02315 ENST00000651006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• 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=-0.8).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00453 (649/143352) while in subpopulation AMR AF = 0.0421 (551/13092). AF 95% confidence interval is 0.0392. There are 141 homozygotes in GnomAd4. There are 351 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 141 gene

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
LINC02315	ENST00000651006.2	n.643-2047C>T		intron_variant	Intron 3 of 3
LINC02315	ENST00000719278.1	n.387-2047C>T		intron_variant	Intron 4 of 4
LINC02315	ENST00000719279.1	n.450-2047C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.00452 AC: 647 AN: 143248 Hom.: 140 Cov.: 28

Gnomad AFR AF: 0.00188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000171

Gnomad OTH AF: 0.00507

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

GnomAD4 genome AF: 0.00453 AC: 649 AN: 143352 Hom.: 141 Cov.: 28 AF XY: 0.00505 AC XY: 351 AN XY: 69482

African (AFR) AF: 0.00187 AC: 77 AN: 41118

American (AMR) AF: 0.0421 AC: 551 AN: 13092

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3406

East Asian (EAS) AF: 0.00 AC: 0 AN: 4870

South Asian (SAS) AF: 0.00 AC: 0 AN: 4544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8950

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.000171 AC: 11 AN: 64198

Other (OTH) AF: 0.00502 AC: 10 AN: 1994

Alfa AF: 0.00237 Hom.: 7

Asia WGS AF: 0.00181 AC: 6 AN: 3336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.24
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs41386945; hg19: chr14-41616231;