12-58517632-C-G

Variant names:

• chr12-58517632-C-G
• rs3913094
• ENST00000849012.1:n.384+4408G>C

Variant summary

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

The ENST00000849012.1(ENSG00000310312):​n.384+4408G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,714 control chromosomes in the GnomAD database, including 5,697 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 0.25 (5697 hom., cov: 31)
• Consequence: ENSG00000310312 ENST00000849012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 7 publications found

Genes affected

ENSG00000310312 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310312	ENST00000849012.1	n.384+4408G>C		intron_variant	Intron 3 of 3
ENSG00000310312	ENST00000849013.1	n.243+10117G>C		intron_variant	Intron 2 of 2
ENSG00000258231	ENST00000849139.1	n.287+3212C>G		intron_variant	Intron 1 of 1
ENSG00000258231	ENST00000849140.1	n.214+1883C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37242 AN: 151596 Hom.: 5688 Cov.: 31

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.246 AC: 37261 AN: 151714 Hom.: 5697 Cov.: 31 AF XY: 0.248 AC XY: 18387 AN XY: 74126

African (AFR) AF: 0.0582 AC: 2411 AN: 41422

American (AMR) AF: 0.324 AC: 4928 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1360 AN: 3460

East Asian (EAS) AF: 0.248 AC: 1278 AN: 5146

South Asian (SAS) AF: 0.290 AC: 1395 AN: 4810

European-Finnish (FIN) AF: 0.329 AC: 3460 AN: 10528

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21385 AN: 67834

Other (OTH) AF: 0.301 AC: 634 AN: 2106

Alfa AF: 0.184 Hom.: 441

Bravo AF: 0.238

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.051
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3913094; hg19: chr12-58911415;