rs6574988

chr14-88093648-T-C

Variant summary

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

The ENST00000654646.1(HISLA):n.403-2851T>C 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 0.912 in 152,154 control chromosomes in the GnomAD database, including 63,398 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 0.91 (63398 hom., cov: 32)
• Consequence: HISLA ENST00000654646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HISLA	ENST00000654646.1	n.403-2851T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138721 AN: 152036 Hom.: 63341 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.912 AC: 138838 AN: 152154 Hom.: 63398 Cov.: 32 AF XY: 0.915 AC XY: 68054 AN XY: 74370

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.909

Alfa AF: 0.913 Hom.: 114595

Bravo AF: 0.913

Asia WGS AF: 0.975 AC: 3391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.1
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6574988; hg19: chr14-88559992; COSMIC: COSV73628071;