chr10-58444842-G-A

Variant names:

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

Variant summary

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

The XR_007062374.1(LOC105378316):​n.95+8636G>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_007062374.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.95+8636G>A		intron_variant	Intron 1 of 3
LOC105378316	XR_945981.3	n.360+9185G>A		intron_variant	Intron 2 of 5
LOC105378316	XR_945982.3	n.360+9185G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;