5-55998500-C-A

Position:

• chr5-55998500-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.388+2946C>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 0.46 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 NR_102755.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL6ST-DT	NR_102755.1	n.388+2946C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL6ST-DT	ENST00000500093.2	n.388+2946C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000645512.1	n.279+4299C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.452

Alfa AF: 0.421 Hom.: 18701

Bravo AF: 0.462

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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