12-57862931-T-G

Variant names:

• chr12-57862931-T-G
• rs10877030
• ENST00000724386.1:n.216+16552T>G

Variant summary

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

The ENST00000724386.1(ENSG00000294563):​n.216+16552T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,898 control chromosomes in the GnomAD database, including 10,218 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 0.35 (10218 hom., cov: 32)
• Consequence: ENSG00000294563 ENST00000724386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 22 publications found

Genes affected

ENSG00000294563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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
ENSG00000294563	ENST00000724386.1	n.216+16552T>G		intron_variant	Intron 1 of 1
ENSG00000294563	ENST00000724387.1	n.238+10084T>G		intron_variant	Intron 1 of 1
ENSG00000294563	ENST00000724388.1	n.95-3696T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53631 AN: 151780 Hom.: 10179 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.354 AC: 53733 AN: 151898 Hom.: 10218 Cov.: 32 AF XY: 0.363 AC XY: 26918 AN XY: 74242

African (AFR) AF: 0.338 AC: 14005 AN: 41410

American (AMR) AF: 0.411 AC: 6267 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3462

East Asian (EAS) AF: 0.728 AC: 3750 AN: 5150

South Asian (SAS) AF: 0.592 AC: 2857 AN: 4824

European-Finnish (FIN) AF: 0.365 AC: 3850 AN: 10556

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21277 AN: 67940

Other (OTH) AF: 0.311 AC: 656 AN: 2112

Alfa AF: 0.336 Hom.: 9773

Bravo AF: 0.355

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs10877030; hg19: chr12-58256714;