rs4899940

Variant names:

• chr14-88087524-A-C
• rs4899940
• ENST00000668342.3:n.1113A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-88087524-A-C
• chr14-88087524-A-G
• chr14-88087524-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000668342.3(HISLA):​n.1113A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: HISLA ENST00000668342.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HISLA	NR_046094.1	n.*178A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HISLA	ENST00000668342.3	n.1113A>C		non_coding_transcript_exon_variant	Exon 3 of 3
HISLA	ENST00000553496.1	n.387-5603A>C		intron_variant	Intron 2 of 2	3
HISLA	ENST00000553929.5	n.328+3369A>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 13151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4899940; hg19: chr14-88553868;