10-120209055-G-C

Variant names:

• chr10-120209055-G-C
• rs914483
• XR_001747605.1:n.624+60G>C

Variant summary

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

The XR_001747605.1(LOC105378515):​n.624+60G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,042 control chromosomes in the GnomAD database, including 15,306 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 0.41 (15306 hom., cov: 32)
• Consequence: LOC105378515 XR_001747605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.971
• Publications: 1 publications found

Genes affected

LOC105378515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 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: 0.414 AC: 62822 AN: 151924 Hom.: 15318 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.413 AC: 62808 AN: 152042 Hom.: 15306 Cov.: 32 AF XY: 0.416 AC XY: 30898 AN XY: 74304

African (AFR) AF: 0.140 AC: 5813 AN: 41486

American (AMR) AF: 0.442 AC: 6757 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3466

East Asian (EAS) AF: 0.327 AC: 1688 AN: 5158

South Asian (SAS) AF: 0.474 AC: 2281 AN: 4814

European-Finnish (FIN) AF: 0.592 AC: 6254 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36364 AN: 67972

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.453 Hom.: 2077

Bravo AF: 0.391

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.68
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs914483; hg19: chr10-121968567;