5-159392607-C-G

Variant names:

• chr5-159392607-C-G
• rs6861600
• ENST00000635333.1:n.327+30C>G

Variant summary

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

The ENST00000641150.1(IL12B-AS1):​n.533-23917C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,066 control chromosomes in the GnomAD database, including 8,051 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 0.32 (8051 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: IL12B-AS1 ENST00000641150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641150.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000635333.1	TSL:5	n.327+30C>G		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.533-23917C>G		intron	N/A
	IL12B-AS1	ENST00000648969.1		n.54-23917C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49109 AN: 151938 Hom.: 8046 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.323 AC: 49139 AN: 152056 Hom.: 8051 Cov.: 32 AF XY: 0.323 AC XY: 24048 AN XY: 74350

African (AFR) AF: 0.323 AC: 13384 AN: 41462

American (AMR) AF: 0.335 AC: 5113 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 997 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2265 AN: 5172

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4826

European-Finnish (FIN) AF: 0.298 AC: 3141 AN: 10556

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21357 AN: 67968

Other (OTH) AF: 0.340 AC: 720 AN: 2116

Alfa AF: 0.308 Hom.: 885

Bravo AF: 0.326

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		0.018

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6861600;

hg19: chr5-158819615;