rs12781751

Variant names:

• chr10-31583898-C-T
• rs12781751
• ENST00000829893.1:n.310+19865G>A

Variant summary

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

The ENST00000829893.1(ENSG00000307931):​n.310+19865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,064 control chromosomes in the GnomAD database, including 20,131 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 0.51 (20131 hom., cov: 33)
• Consequence: ENSG00000307931 ENST00000829893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 5 publications found

Genes affected

ENSG00000307931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829893.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307931	ENST00000829893.1		n.310+19865G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77834 AN: 151946 Hom.: 20102 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.512 AC: 77912 AN: 152064 Hom.: 20131 Cov.: 33 AF XY: 0.505 AC XY: 37564 AN XY: 74312

African (AFR) AF: 0.485 AC: 20116 AN: 41474

American (AMR) AF: 0.576 AC: 8803 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2314 AN: 5162

South Asian (SAS) AF: 0.392 AC: 1893 AN: 4826

European-Finnish (FIN) AF: 0.443 AC: 4676 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36848 AN: 67980

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.535 Hom.: 36445

Bravo AF: 0.528

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs12781751; hg19: chr10-31872826;