10-44392481-G-A

Variant names:

• chr10-44392481-G-A
• rs7088285
• ENST00000791650.1:n.52-5676G>A

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.52-5676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,324 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3456 hom., cov: 31)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984179	XR_001747298.2	n.67+2649G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303087	ENST00000791650.1	n.52-5676G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30550 AN: 151208 Hom.: 3446 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.202 AC: 30581 AN: 151324 Hom.: 3456 Cov.: 31 AF XY: 0.204 AC XY: 15044 AN XY: 73900

African (AFR) AF: 0.130 AC: 5364 AN: 41166

American (AMR) AF: 0.209 AC: 3180 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 928 AN: 3456

East Asian (EAS) AF: 0.432 AC: 2216 AN: 5130

South Asian (SAS) AF: 0.279 AC: 1323 AN: 4750

European-Finnish (FIN) AF: 0.201 AC: 2106 AN: 10468

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14677 AN: 67846

Other (OTH) AF: 0.237 AC: 495 AN: 2090

Alfa AF: 0.139 Hom.: 395

Bravo AF: 0.198

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.60
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7088285; hg19: chr10-44887929;