rs7709212

Variant names:

• chr5-159337169-T-C
• rs7709212
• ENST00000515337.1:n.745+4166T>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+4166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,000 control chromosomes in the GnomAD database, including 9,190 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 (9190 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 42 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.745+4166T>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+4166T>C		intron_variant	Intron 2 of 4	2
ENSG00000249738	ENST00000641150.1	n.324+4166T>C		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000764988.1	n.566+4166T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51947 AN: 151882 Hom.: 9174 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.342 AC: 51988 AN: 152000 Hom.: 9190 Cov.: 32 AF XY: 0.344 AC XY: 25573 AN XY: 74310

African (AFR) AF: 0.301 AC: 12457 AN: 41372

American (AMR) AF: 0.452 AC: 6905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2481 AN: 5174

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3381 AN: 10586

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

European-Non Finnish (NFE) AF: 0.336 AC: 22827 AN: 67970

Other (OTH) AF: 0.368 AC: 779 AN: 2116

Alfa AF: 0.344 Hom.: 35387

Bravo AF: 0.353

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs7709212; hg19: chr5-158764177;