14-58776620-A-G

Variant names:

• chr14-58776620-A-G
• rs10149208
• ENST00000648996.1:n.607+9960A>G

Variant summary

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

The ENST00000648996.1(LINC01500):​n.607+9960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.63 (27786 hom., cov: 18)
• Consequence: LINC01500 ENST00000648996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 4 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

ENSG00000301175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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
LINC01500	ENST00000648996.1	n.607+9960A>G		intron_variant	Intron 4 of 13
ENSG00000301175	ENST00000776815.1	n.210-1970T>C		intron_variant	Intron 1 of 2
ENSG00000301175	ENST00000776816.1	n.351-1970T>C		intron_variant	Intron 2 of 3
ENSG00000301175	ENST00000776817.1	n.144-1970T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.630 AC: 86554 AN: 137320 Hom.: 27780 Cov.: 18

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.630 AC: 86617 AN: 137438 Hom.: 27786 Cov.: 18 AF XY: 0.629 AC XY: 41251 AN XY: 65596

African (AFR) AF: 0.749 AC: 26820 AN: 35802

American (AMR) AF: 0.521 AC: 6847 AN: 13140

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2004 AN: 3362

East Asian (EAS) AF: 0.808 AC: 3753 AN: 4646

South Asian (SAS) AF: 0.477 AC: 1833 AN: 3840

European-Finnish (FIN) AF: 0.620 AC: 5329 AN: 8602

Middle Eastern (MID) AF: 0.597 AC: 173 AN: 290

European-Non Finnish (NFE) AF: 0.587 AC: 38175 AN: 65024

Other (OTH) AF: 0.620 AC: 1154 AN: 1860

Alfa AF: 0.603 Hom.: 110318

Bravo AF: 0.637

Asia WGS AF: 0.612 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.43
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10149208; hg19: chr14-59243338;