chr10-120208932-G-A

Variant names:

• chr10-120208932-G-A
• rs12263503
• XR_001747605.1:n.561G>A

Variant summary

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

The XR_001747605.1(LOC105378515):​n.561G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,190 control chromosomes in the GnomAD database, including 627 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 0.089 (627 hom., cov: 32)
• Consequence: LOC105378515 XR_001747605.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 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: 0.0892 AC: 13560 AN: 152072 Hom.: 625 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0891 AC: 13565 AN: 152190 Hom.: 627 Cov.: 32 AF XY: 0.0874 AC XY: 6504 AN XY: 74400

African (AFR) AF: 0.0848 AC: 3522 AN: 41512

American (AMR) AF: 0.0922 AC: 1409 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.0656 AC: 316 AN: 4814

European-Finnish (FIN) AF: 0.0722 AC: 765 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6924 AN: 67998

Other (OTH) AF: 0.0913 AC: 193 AN: 2114

Alfa AF: 0.0985 Hom.: 150

Bravo AF: 0.0910

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12263503; hg19: chr10-121968444;