rs11186286

chr10-90717319-T-C

Variant summary

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

The XR_007062237.1(LOC124902478):n.3373A>G 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 0.204 in 152,048 control chromosomes in the GnomAD database, including 3,768 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 0.20 (3768 hom., cov: 32)
• Consequence: LOC124902478 XR_007062237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

Genes affected

LOC124902478 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902478	XR_007062237.1	n.3373A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31039 AN: 151930 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.204 AC: 31074 AN: 152048 Hom.: 3768 Cov.: 32 AF XY: 0.198 AC XY: 14704 AN XY: 74338

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0638

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.194

Alfa AF: 0.176 Hom.: 5102

Bravo AF: 0.213

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.9
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11186286; hg19: chr10-92477076;