rs6574988

Variant names:

• chr14-88093648-T-C
• rs6574988
• ENST00000553929.5:n.329-2851T>C

Variant summary

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

The ENST00000553929.5(HISLA):​n.329-2851T>C variant causes a intron 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 ENST00000553929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553929.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HISLA	ENST00000553929.5	TSL:3	n.329-2851T>C		intron	N/A
	HISLA	ENST00000556673.2	TSL:3	n.62-2851T>C		intron	N/A
	HISLA	ENST00000653288.1		n.505-2851T>C		intron	N/A

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

African (AFR) AF: 0.890 AC: 36945 AN: 41526

American (AMR) AF: 0.939 AC: 14327 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3154 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5162

South Asian (SAS) AF: 0.945 AC: 4554 AN: 4820

European-Finnish (FIN) AF: 0.914 AC: 9701 AN: 10612

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 61984 AN: 67980

Other (OTH) AF: 0.909 AC: 1921 AN: 2114

Alfa AF: 0.912 Hom.: 180718

Bravo AF: 0.913

Asia WGS AF: 0.975 AC: 3391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.25
PhyloP100		0.42

Splicing

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

Other links and lift over

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