10-121217052-C-G

Variant names:

• chr10-121217052-C-G
• rs10749409
• XR_007062321.1:n.516-23442G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062321.1(LOC105378523):​n.516-23442G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,962 control chromosomes in the GnomAD database, including 36,503 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 0.69 (36503 hom., cov: 31)
• Consequence: LOC105378523 XR_007062321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05

Genes affected

LOC105378523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378523	XR_007062321.1	n.516-23442G>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105069 AN: 151844 Hom.: 36454 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.692 AC: 105180 AN: 151962 Hom.: 36503 Cov.: 31 AF XY: 0.695 AC XY: 51613 AN XY: 74260

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.677

Alfa AF: 0.690 Hom.: 4515

Bravo AF: 0.702

Asia WGS AF: 0.682 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0080
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10749409; hg19: chr10-122976566;