chr5-55998500-C-A

Variant names:

• chr5-55998500-C-A
• rs6870870
• ENST00000500093.3:n.404+2946C>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.404+2946C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,982 control chromosomes in the GnomAD database, including 17,431 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 0.46 (17431 hom., cov: 31)
• Consequence: IL6ST-DT ENST00000500093.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500093.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL6ST-DT	NR_102755.1		n.388+2946C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL6ST-DT	ENST00000500093.3	TSL:1	n.404+2946C>A		intron	N/A
	ENSG00000249236	ENST00000645512.1		n.279+4299C>A		intron	N/A
	IL6ST-DT	ENST00000686866.3		n.667+2681C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69848 AN: 151864 Hom.: 17393 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.460 AC: 69937 AN: 151982 Hom.: 17431 Cov.: 31 AF XY: 0.451 AC XY: 33503 AN XY: 74276

African (AFR) AF: 0.637 AC: 26395 AN: 41446

American (AMR) AF: 0.344 AC: 5255 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3466

East Asian (EAS) AF: 0.128 AC: 666 AN: 5184

South Asian (SAS) AF: 0.349 AC: 1677 AN: 4804

European-Finnish (FIN) AF: 0.434 AC: 4573 AN: 10532

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28284 AN: 67952

Other (OTH) AF: 0.452 AC: 957 AN: 2116

Alfa AF: 0.428 Hom.: 24549

Bravo AF: 0.462

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.62
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6870870; hg19: chr5-55294328; COSMIC: COSV67179184;