rs10487245

Variant names:

• chr7-94084209-G-A
• rs10487245
• ENST00000834140.1:n.441+6534C>T

Variant summary

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

The ENST00000834140.1(ENSG00000285090):​n.441+6534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 152,210 control chromosomes in the GnomAD database, including 787 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 0.085 (787 hom., cov: 32)
• Consequence: ENSG00000285090 ENST00000834140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 6 publications found

Genes affected

ENSG00000285090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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
ENSG00000285090	ENST00000834140.1	n.441+6534C>T		intron_variant	Intron 4 of 4
ENSG00000285090	ENST00000834141.1	n.322+6534C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12913 AN: 152092 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0851 AC: 12949 AN: 152210 Hom.: 787 Cov.: 32 AF XY: 0.0854 AC XY: 6353 AN XY: 74416

African (AFR) AF: 0.154 AC: 6374 AN: 41506

American (AMR) AF: 0.120 AC: 1839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.138 AC: 716 AN: 5178

South Asian (SAS) AF: 0.104 AC: 503 AN: 4820

European-Finnish (FIN) AF: 0.0254 AC: 269 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0421 AC: 2865 AN: 68030

Other (OTH) AF: 0.0785 AC: 166 AN: 2114

Alfa AF: 0.0678 Hom.: 980

Bravo AF: 0.0950

Asia WGS AF: 0.127 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	15
DANN	Benign	0.44
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs10487245; hg19: chr7-93713521;