ENST00000635333.1:n.327+3060G>C

Variant names:

• chr5-159395637-G-C
• rs6887695
• ENST00000635333.1:n.327+3060G>C

Variant summary

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

The ENST00000635333.1(IL12B-AS1):​n.327+3060G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,962 control chromosomes in the GnomAD database, including 9,329 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 0.35 (9329 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 152 publications found

Genes affected

IL12B-AS1 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635333.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000635333.1	TSL:5	n.327+3060G>C		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.533-20887G>C		intron	N/A
	IL12B-AS1	ENST00000648969.1		n.54-20887G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52573 AN: 151844 Hom.: 9315 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.346 AC: 52621 AN: 151962 Hom.: 9329 Cov.: 32 AF XY: 0.346 AC XY: 25693 AN XY: 74262

African (AFR) AF: 0.407 AC: 16841 AN: 41416

American (AMR) AF: 0.341 AC: 5202 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2211 AN: 5168

South Asian (SAS) AF: 0.365 AC: 1762 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3133 AN: 10560

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21335 AN: 67938

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.322 Hom.: 4297

Bravo AF: 0.353

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs6887695; hg19: chr5-158822645;