rs7085387

Variant names:

• chr10-58444842-G-A
• rs7085387
• XR_007062374.1:n.95+8636G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-58444842-G-A
• chr10-58444842-G-C
• chr10-58444842-G-T

Variant summary

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

The XR_945981.3(LOC105378316):​n.360+9185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,834 control chromosomes in the GnomAD database, including 32,903 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 0.64 (32903 hom., cov: 30)
• Consequence: LOC105378316 XR_945981.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 4 publications found

Genes affected

LOC105378316 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96726 AN: 151716 Hom.: 32891 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.637 AC: 96769 AN: 151834 Hom.: 32903 Cov.: 30 AF XY: 0.636 AC XY: 47223 AN XY: 74206

African (AFR) AF: 0.379 AC: 15652 AN: 41344

American (AMR) AF: 0.738 AC: 11267 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2394 AN: 3466

East Asian (EAS) AF: 0.662 AC: 3417 AN: 5162

South Asian (SAS) AF: 0.560 AC: 2689 AN: 4800

European-Finnish (FIN) AF: 0.699 AC: 7361 AN: 10528

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.762 AC: 51773 AN: 67964

Other (OTH) AF: 0.635 AC: 1336 AN: 2104

Alfa AF: 0.715 Hom.: 20289

Bravo AF: 0.634

Asia WGS AF: 0.566 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.34
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs7085387; hg19: chr10-60204602;