rs12263503

Positions:

• chr10-120208932-G-A

Variant summary

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

The XR_001747606.1(LOC105378515):​n.852G>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_001747606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

LOC105378515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378515	XR_001747606.1	n.852G>A		non_coding_transcript_exon_variant	6/8
LOC105378515	XR_001747605.1	n.561G>A		non_coding_transcript_exon_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.0922

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0656

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0913

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12263503; hg19: chr10-121968444;