12-31112991-C-G

Variant names:

• chr12-31112991-C-G
• rs2302850
• ENST00000391394.4:n.575G>C

Variant summary

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

The ENST00000391394.4(ENSG00000291250):​n.575G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 153,752 control chromosomes in the GnomAD database, including 22,447 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 0.53 (22028 hom., cov: 30)
  • Exomes 𝑓: 0.53 (419 hom.)
• Consequence: ENSG00000291250 ENST00000391394.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 12 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVOS2P	NR_153414.1	n.5557G>C		non_coding_transcript_exon_variant	Exon 44 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291250	ENST00000391394.4	n.575G>C		non_coding_transcript_exon_variant	Exon 6 of 7	1
ENSG00000291250	ENST00000542490.5	n.919G>C		non_coding_transcript_exon_variant	Exon 6 of 8	5
ENSG00000291250	ENST00000542925.8	n.854G>C		non_coding_transcript_exon_variant	Exon 6 of 7	2

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80233 AN: 150804 Hom.: 21974 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.529 AC: 1499 AN: 2832 Hom.: 419 Cov.: 0 AF XY: 0.534 AC XY: 770 AN XY: 1442

African (AFR) AF: 0.667 AC: 44 AN: 66

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.570 AC: 49 AN: 86

European-Finnish (FIN) AF: 0.408 AC: 260 AN: 638

Middle Eastern (MID) AF: 0.583 AC: 947 AN: 1624

European-Non Finnish (NFE) AF: 0.370 AC: 40 AN: 108

Other (OTH) AF: 0.513 AC: 156 AN: 304

GnomAD4 genome AF: 0.532 AC: 80339 AN: 150920 Hom.: 22028 Cov.: 30 AF XY: 0.535 AC XY: 39396 AN XY: 73650

African (AFR) AF: 0.672 AC: 27612 AN: 41092

American (AMR) AF: 0.591 AC: 8968 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1359 AN: 3458

East Asian (EAS) AF: 0.838 AC: 4319 AN: 5156

South Asian (SAS) AF: 0.568 AC: 2712 AN: 4774

European-Finnish (FIN) AF: 0.408 AC: 4238 AN: 10392

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29520 AN: 67598

Other (OTH) AF: 0.520 AC: 1084 AN: 2086

Alfa AF: 0.487 Hom.: 1978

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-0.16
Mutation Taster		=46/54	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2302850; hg19: chr12-31265925;