10-120103958-G-A

Variant names:

• chr10-120103958-G-A
• rs10510060
• XR_007062313.1:n.-29C>T

Variant summary

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

The XR_007062313.1(LOC124902514):​n.-29C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,194 control chromosomes in the GnomAD database, including 478 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 0.063 (478 hom., cov: 32)
• Consequence: LOC124902514 XR_007062313.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 1 publications found

Genes affected

LOC124902514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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: 0.0627 AC: 9533 AN: 152076 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0289

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0627 AC: 9536 AN: 152194 Hom.: 478 Cov.: 32 AF XY: 0.0646 AC XY: 4806 AN XY: 74406

African (AFR) AF: 0.0141 AC: 586 AN: 41538

American (AMR) AF: 0.0556 AC: 849 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5172

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4822

European-Finnish (FIN) AF: 0.0622 AC: 659 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5521 AN: 67996

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0728 Hom.: 655

Bravo AF: 0.0537

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.022
DANN	Benign	0.46
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10510060; hg19: chr10-121863470;