rs12148658

Positions:

• chr15-37876078-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0971 in 152,044 control chromosomes in the GnomAD database, including 860 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 0.097 (860 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37876078G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14760 AN: 151926 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0971 AC: 14763 AN: 152044 Hom.: 860 Cov.: 32 AF XY: 0.0996 AC XY: 7401 AN XY: 74304

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.112

Alfa AF: 0.117 Hom.: 296

Bravo AF: 0.0901

Asia WGS AF: 0.0600 AC: 209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12148658; hg19: chr15-38168279;