rs953861

Variant names:

• chr5-159345574-G-A
• rs953861
• ENST00000515337.1:n.746-1942G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-159345574-G-A
• chr5-159345574-G-C

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.746-1942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,200 control chromosomes in the GnomAD database, including 60,332 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 0.89 (60332 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 16 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.746-1942G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.746-1942G>A		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.325-1942G>A		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000764988.1	n.567-8430G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135103 AN: 152082 Hom.: 60270 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.888 AC: 135225 AN: 152200 Hom.: 60332 Cov.: 31 AF XY: 0.892 AC XY: 66347 AN XY: 74420

African (AFR) AF: 0.969 AC: 40254 AN: 41522

American (AMR) AF: 0.904 AC: 13830 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2972 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5178

South Asian (SAS) AF: 0.891 AC: 4290 AN: 4816

European-Finnish (FIN) AF: 0.860 AC: 9110 AN: 10596

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56718 AN: 68002

Other (OTH) AF: 0.887 AC: 1872 AN: 2110

Alfa AF: 0.846 Hom.: 85202

Bravo AF: 0.897

Asia WGS AF: 0.954 AC: 3318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs953861; hg19: chr5-158772582;