rs62377586

Variant names:

• chr5-159339014-G-A
• rs62377586
• ENST00000515337.1:n.745+6011G>A

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.745+6011G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,648 control chromosomes in the GnomAD database, including 8,200 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 0.33 (8200 hom., cov: 29)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.745+6011G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.745+6011G>A		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.324+6011G>A		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000764988.1	n.566+6011G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49433 AN: 151530 Hom.: 8197 Cov.: 29

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.326 AC: 49455 AN: 151648 Hom.: 8200 Cov.: 29 AF XY: 0.326 AC XY: 24171 AN XY: 74064

African (AFR) AF: 0.296 AC: 12214 AN: 41292

American (AMR) AF: 0.347 AC: 5291 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3462

East Asian (EAS) AF: 0.424 AC: 2187 AN: 5152

South Asian (SAS) AF: 0.368 AC: 1764 AN: 4792

European-Finnish (FIN) AF: 0.320 AC: 3352 AN: 10480

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22574 AN: 67918

Other (OTH) AF: 0.348 AC: 730 AN: 2100

Alfa AF: 0.323 Hom.: 1079

Bravo AF: 0.326

Asia WGS AF: 0.423 AC: 1456 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.78
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs62377586; hg19: chr5-158766022;