rs728142

Variant names:

• chr10-44394011-G-A
• rs728142
• ENST00000791650.1:n.52-4146G>A

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.52-4146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 152,244 control chromosomes in the GnomAD database, including 391 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 0.069 (391 hom., cov: 33)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 2 publications found

Genes affected

ENSG00000303087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984179	XR_001747298.2	n.68-4146G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303087	ENST00000791650.1	n.52-4146G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10497 AN: 152126 Hom.: 392 Cov.: 33

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0689 AC: 10495 AN: 152244 Hom.: 391 Cov.: 33 AF XY: 0.0690 AC XY: 5136 AN XY: 74422

African (AFR) AF: 0.0345 AC: 1432 AN: 41556

American (AMR) AF: 0.0761 AC: 1163 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3468

East Asian (EAS) AF: 0.0945 AC: 489 AN: 5174

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4822

European-Finnish (FIN) AF: 0.0721 AC: 765 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5910 AN: 68004

Other (OTH) AF: 0.0912 AC: 193 AN: 2116

Alfa AF: 0.0708 Hom.: 62

Bravo AF: 0.0686

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.67
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs728142; hg19: chr10-44889459;