14-88087524-A-G

Position:

• chr14-88087524-A-G

Variant summary

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

The ENST00000654646.1(HISLA):​n.402+3369A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,730 control chromosomes in the GnomAD database, including 23,779 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 0.56 (23779 hom., cov: 31)
• Consequence: HISLA ENST00000654646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

HISLA (HGNC:49467): (HIF1A stabilizing long noncoding RNA)

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 (NFE) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HISLA	ENST00000654646.1	n.402+3369A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84172 AN: 151612 Hom.: 23775 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.555 AC: 84211 AN: 151730 Hom.: 23779 Cov.: 31 AF XY: 0.556 AC XY: 41259 AN XY: 74174

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.546

Alfa AF: 0.569 Hom.: 11712

Bravo AF: 0.545

Asia WGS AF: 0.492 AC: 1715 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	4.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899940; hg19: chr14-88553868;