chr10-120103958-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902514	XR_007062313.1	n.-29C>T		upstream_gene_variant

Ensembl

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

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 v4.3

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;