chr14-59163821-T-C

Position:

• chr14-59163821-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657369.1(LINC01500):​n.716-19842T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,110 control chromosomes in the GnomAD database, including 40,802 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 0.73 (40802 hom., cov: 32)
• Consequence: LINC01500 ENST00000657369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

LINC01500 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984642	XR_001750928.1	n.41+5637T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000657369.1	n.716-19842T>C		intron_variant
LINC01500	ENST00000663641.1	n.830-19842T>C		intron_variant
LINC01500	ENST00000665985.1	n.693-19842T>C		intron_variant
LINC01500	ENST00000666814.1	n.641-19842T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111144 AN: 151992 Hom.: 40751 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.731 AC: 111250 AN: 152110 Hom.: 40802 Cov.: 32 AF XY: 0.726 AC XY: 53943 AN XY: 74350

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.729

Alfa AF: 0.723 Hom.: 25489

Bravo AF: 0.740

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6573249; hg19: chr14-59630539; COSMIC: COSV53415569;