14-88120776-T-C

Variant names:

• chr14-88120776-T-C
• rs11159841
• ENST00000656018.2:n.1562-20280T>C

Variant summary

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

The ENST00000656018.2(HISLA):​n.1562-20280T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 136,578 control chromosomes in the GnomAD database, including 9,102 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 0.34 (9102 hom., cov: 25)
• Consequence: HISLA ENST00000656018.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656018.2. 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	ENST00000656018.2		n.1562-20280T>C		intron	N/A
	HISLA	ENST00000828315.1		n.241-20280T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 45849 AN: 136548 Hom.: 9107 Cov.: 25

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.336 AC: 45828 AN: 136578 Hom.: 9102 Cov.: 25 AF XY: 0.338 AC XY: 22098 AN XY: 65418

African (AFR) AF: 0.107 AC: 3917 AN: 36480

American (AMR) AF: 0.393 AC: 5200 AN: 13248

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1394 AN: 3316

East Asian (EAS) AF: 0.491 AC: 2247 AN: 4578

South Asian (SAS) AF: 0.421 AC: 1857 AN: 4416

European-Finnish (FIN) AF: 0.412 AC: 2922 AN: 7100

Middle Eastern (MID) AF: 0.419 AC: 104 AN: 248

European-Non Finnish (NFE) AF: 0.421 AC: 27133 AN: 64446

Other (OTH) AF: 0.362 AC: 680 AN: 1876

Alfa AF: 0.376 Hom.: 5258

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11159841;

hg19: chr14-88587120;