rs715180

chr5-56001471-C-A

Variant summary

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

The NR_102755.1(IL6ST-DT):n.389-278C>A 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 0.926 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 NR_102755.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IL6ST-DT	NR_102755.1	n.389-278C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL6ST-DT	ENST00000500093.2	n.389-278C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000645512.1	n.279+7270C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.905

Alfa AF: 0.921 Hom.: 86169

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs715180; hg19: chr5-55297299;