10-57386706-T-C

Variant names:

• chr10-57386706-T-C
• rs2928442
• ENST00000812047.1:n.75+20531A>G

Variant summary

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

The ENST00000812047.1(ENSG00000305625):​n.75+20531A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,814 control chromosomes in the GnomAD database, including 1,877 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 0.12 (1877 hom., cov: 32)
• Consequence: ENSG00000305625 ENST00000812047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 2 publications found

Genes affected

ENSG00000305625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1	n.63-10600A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305625	ENST00000812047.1	n.75+20531A>G		intron_variant	Intron 2 of 2
ENSG00000305625	ENST00000812048.1	n.63-10600A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18181 AN: 151704 Hom.: 1872 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.120 AC: 18218 AN: 151814 Hom.: 1877 Cov.: 32 AF XY: 0.122 AC XY: 9016 AN XY: 74182

African (AFR) AF: 0.268 AC: 11092 AN: 41348

American (AMR) AF: 0.191 AC: 2914 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.0957 AC: 494 AN: 5162

South Asian (SAS) AF: 0.0811 AC: 390 AN: 4810

European-Finnish (FIN) AF: 0.0295 AC: 311 AN: 10542

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.0382 AC: 2596 AN: 67948

Other (OTH) AF: 0.106 AC: 222 AN: 2104

Alfa AF: 0.0998 Hom.: 254

Bravo AF: 0.139

Asia WGS AF: 0.105 AC: 366 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2928442; hg19: chr10-59146466;