14-85497512-C-A

Variant names:

• chr14-85497512-C-A
• rs8014131
• ENST00000557547.1:n.110+19313G>T

Variant summary

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

The ENST00000557547.1(ENSG00000258902):​n.110+19313G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,912 control chromosomes in the GnomAD database, including 13,222 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 0.42 (13222 hom., cov: 32)
• Consequence: ENSG00000258902 ENST00000557547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

ENSG00000258902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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
ENSG00000258902	ENST00000557547.1	n.110+19313G>T		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63034 AN: 151794 Hom.: 13208 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.415 AC: 63075 AN: 151912 Hom.: 13222 Cov.: 32 AF XY: 0.411 AC XY: 30527 AN XY: 74246

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.427

Alfa AF: 0.427 Hom.: 17001

Bravo AF: 0.418

Asia WGS AF: 0.412 AC: 1430 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8014131; hg19: chr14-85963856;