rs4931434

Variant names:

• chr12-31113353-C-A
• rs4931434
• ENST00000391394.4:n.483-270G>T

Variant summary

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

The ENST00000391394.4(ENSG00000291250):​n.483-270G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,838 control chromosomes in the GnomAD database, including 13,007 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 0.41 (13007 hom., cov: 32)
• Consequence: ENSG00000291250 ENST00000391394.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 15 publications found

Genes affected

ENSG00000291250 (HGNC:):

ENSG00000177359 (HGNC:34046):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVOS2P	NR_153414.1	n.5465-270G>T		intron_variant	Intron 43 of 44

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291250	ENST00000391394.4	n.483-270G>T		intron_variant	Intron 5 of 6	1
ENSG00000291250	ENST00000542490.5	n.827-270G>T		intron_variant	Intron 5 of 7	5
ENSG00000291250	ENST00000542925.8	n.762-270G>T		intron_variant	Intron 5 of 6	2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61440 AN: 151720 Hom.: 12975 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.405 AC: 61518 AN: 151838 Hom.: 13007 Cov.: 32 AF XY: 0.409 AC XY: 30335 AN XY: 74202

African (AFR) AF: 0.484 AC: 20047 AN: 41406

American (AMR) AF: 0.509 AC: 7769 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3466

East Asian (EAS) AF: 0.773 AC: 3980 AN: 5150

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3451 AN: 10546

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22089 AN: 67882

Other (OTH) AF: 0.378 AC: 796 AN: 2104

Alfa AF: 0.352 Hom.: 32170

Asia WGS AF: 0.566 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.70
PhyloP100		-1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4931434; hg19: chr12-31266287;