rs10065906

Variant names:

• chr5-159580770-C-A
• rs10065906
• ENST00000636819.1:n.44+27725C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-159580770-C-A
• chr5-159580770-C-G
• chr5-159580770-C-T

Variant summary

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

The ENST00000642094.1(IL12B-AS1):​n.323+335C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,104 control chromosomes in the GnomAD database, including 41,750 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 0.73 (41750 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000642094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 13 publications found

Genes affected

IL12B-AS1 (HGNC:58156):

LOC105377684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642094.1. 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	ENST00000636819.1	TSL:5	n.44+27725C>A		intron	N/A
	IL12B-AS1	ENST00000642094.1		n.323+335C>A		intron	N/A
	IL12B-AS1	ENST00000811686.1		n.92+27725C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111342 AN: 151986 Hom.: 41695 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.733 AC: 111457 AN: 152104 Hom.: 41750 Cov.: 32 AF XY: 0.725 AC XY: 53900 AN XY: 74328

African (AFR) AF: 0.894 AC: 37133 AN: 41544

American (AMR) AF: 0.678 AC: 10355 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2306 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3613 AN: 5174

South Asian (SAS) AF: 0.553 AC: 2649 AN: 4792

European-Finnish (FIN) AF: 0.633 AC: 6685 AN: 10562

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46236 AN: 67974

Other (OTH) AF: 0.742 AC: 1559 AN: 2102

Alfa AF: 0.696 Hom.: 132749

Bravo AF: 0.744

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		-0.020

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: rs10065906;

hg19: chr5-159007778;