rs4931443

Variant names:

• chr12-31125097-T-A
• rs4931443
• ENST00000641844.2:n.5207+274A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-31125097-T-A
• chr12-31125097-T-G

Variant summary

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

The NR_153414.1(OVOS2P):​n.4867+274A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,272 control chromosomes in the GnomAD database, including 62,602 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 0.91 (62602 hom., cov: 33)
• Consequence: OVOS2P NR_153414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 3 publications found

Genes affected

ENSG00000177359 (HGNC:34046):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_153414.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OVOS2P	NR_153414.1		n.4867+274A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000177359	ENST00000641844.2		n.5207+274A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137869 AN: 152154 Hom.: 62546 Cov.: 33

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.906 AC: 137980 AN: 152272 Hom.: 62602 Cov.: 33 AF XY: 0.908 AC XY: 67597 AN XY: 74454

African (AFR) AF: 0.849 AC: 35254 AN: 41534

American (AMR) AF: 0.914 AC: 13982 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3040 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4881 AN: 5176

South Asian (SAS) AF: 0.922 AC: 4441 AN: 4818

European-Finnish (FIN) AF: 0.948 AC: 10067 AN: 10616

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63336 AN: 68034

Other (OTH) AF: 0.901 AC: 1902 AN: 2112

Alfa AF: 0.922 Hom.: 8025

Bravo AF: 0.901

Asia WGS AF: 0.935 AC: 3251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.5
DANN	Benign	0.52
PhyloP100		0.56

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: rs4931443; hg19: chr12-31278031;