rs715180

Variant names:

• chr5-56001471-C-A
• rs715180
• ENST00000500093.3:n.405-278C>A

Variant summary

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

The ENST00000500093.3(IL6ST-DT):​n.405-278C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,340 control chromosomes in the GnomAD database, including 65,639 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 0.93 (65639 hom., cov: 34)
• Consequence: IL6ST-DT ENST00000500093.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 7 publications found

Genes affected

IL6ST-DT (HGNC:55804): (IL6ST divergent transcript)

ENSG00000249236 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL6ST-DT	NR_102755.1	n.389-278C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL6ST-DT	ENST00000500093.3	n.405-278C>A		intron_variant	Intron 1 of 1	1
ENSG00000249236	ENST00000645512.1	n.279+7270C>A		intron_variant	Intron 2 of 3
IL6ST-DT	ENST00000686866.3	n.668-278C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140939 AN: 152222 Hom.: 65574 Cov.: 34

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.926 AC: 141064 AN: 152340 Hom.: 65639 Cov.: 34 AF XY: 0.922 AC XY: 68659 AN XY: 74494

African (AFR) AF: 0.984 AC: 40935 AN: 41584

American (AMR) AF: 0.854 AC: 13068 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3177 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3496 AN: 5182

South Asian (SAS) AF: 0.863 AC: 4165 AN: 4828

European-Finnish (FIN) AF: 0.938 AC: 9957 AN: 10616

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63274 AN: 68044

Other (OTH) AF: 0.905 AC: 1914 AN: 2116

Alfa AF: 0.920 Hom.: 119661

Bravo AF: 0.920

Asia WGS AF: 0.805 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.18
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs715180; hg19: chr5-55297299;