chr10-20385724-A-G

Variant names:

• chr10-20385724-A-G
• rs12772794
• ENST00000785943.1:n.285+14969A>G

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.285+14969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,116 control chromosomes in the GnomAD database, including 11,088 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 0.36 (11088 hom., cov: 32)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 10 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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
ENSG00000302338	ENST00000785943.1	n.285+14969A>G		intron_variant	Intron 1 of 5
ENSG00000302338	ENST00000785944.1	n.198+14969A>G		intron_variant	Intron 1 of 3
ENSG00000302338	ENST00000785945.1	n.132+14969A>G		intron_variant	Intron 1 of 4
ENSG00000302338	ENST00000785947.1	n.41+14969A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54151 AN: 151998 Hom.: 11088 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.356 AC: 54152 AN: 152116 Hom.: 11088 Cov.: 32 AF XY: 0.361 AC XY: 26872 AN XY: 74354

African (AFR) AF: 0.146 AC: 6049 AN: 41530

American (AMR) AF: 0.420 AC: 6420 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2863 AN: 5160

South Asian (SAS) AF: 0.424 AC: 2046 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4676 AN: 10576

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29555 AN: 67954

Other (OTH) AF: 0.358 AC: 758 AN: 2116

Alfa AF: 0.400 Hom.: 36663

Bravo AF: 0.344

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12772794; hg19: chr10-20674653;