rs6556412

Variant names:

• chr5-159360377-G-A
• rs6556412
• ENST00000515337.1:n.954-1831G>A

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.954-1831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,092 control chromosomes in the GnomAD database, including 8,686 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 0.34 (8686 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 48 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.954-1831G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.954-1831G>A		intron_variant	Intron 4 of 4	2
ENSG00000249738	ENST00000635333.1	n.282+6256G>A		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.532+6256G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51120 AN: 151972 Hom.: 8680 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.336 AC: 51153 AN: 152092 Hom.: 8686 Cov.: 32 AF XY: 0.336 AC XY: 24980 AN XY: 74328

African (AFR) AF: 0.334 AC: 13856 AN: 41470

American (AMR) AF: 0.351 AC: 5372 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2310 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1772 AN: 4822

European-Finnish (FIN) AF: 0.307 AC: 3247 AN: 10566

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22476 AN: 67980

Other (OTH) AF: 0.352 AC: 745 AN: 2114

Alfa AF: 0.334 Hom.: 31423

Bravo AF: 0.338

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6556412; hg19: chr5-158787385;