rs12115454

chr9-115957771-G-A

Variant summary

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

The XR_007061749.1(LOC124902258):n.1795G>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 0.099 in 151,644 control chromosomes in the GnomAD database, including 809 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 0.099 (809 hom., cov: 31)
• Consequence: LOC124902258 XR_007061749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

Genes affected

LOC124902258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902258	XR_007061749.1	n.1795G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15011 AN: 151538 Hom.: 808 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0990 AC: 15019 AN: 151644 Hom.: 809 Cov.: 31 AF XY: 0.0966 AC XY: 7155 AN XY: 74048

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0203

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0940 Hom.: 982

Bravo AF: 0.111

Asia WGS AF: 0.118 AC: 410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.3
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12115454; hg19: chr9-118720050;