rs6868898

Variant names:

• chr5-159337412-T-C
• rs6868898
• ENST00000515337.1:n.745+4409T>C

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.745+4409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,110 control chromosomes in the GnomAD database, including 7,822 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 0.31 (7822 hom., cov: 33)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 12 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.745+4409T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.745+4409T>C		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.324+4409T>C		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000764988.1	n.566+4409T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47240 AN: 151990 Hom.: 7810 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.311 AC: 47294 AN: 152110 Hom.: 7822 Cov.: 33 AF XY: 0.318 AC XY: 23675 AN XY: 74344

African (AFR) AF: 0.222 AC: 9222 AN: 41510

American (AMR) AF: 0.382 AC: 5845 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1826 AN: 5180

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4500 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22521 AN: 67962

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.313 Hom.: 8684

Bravo AF: 0.304

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6868898; hg19: chr5-158764420;