chr7-15185914-G-T

Position:

• chr7-15185914-G-T

Variant summary

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

The XM_011515402.4(AGMO):​c.1264-26451C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,054 control chromosomes in the GnomAD database, including 3,884 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 0.22 (3884 hom., cov: 33)
• Consequence: AGMO XM_011515402.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

Genes affected

AGMO (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGMO	XM_011515402.4	c.1264-26451C>A		intron_variant			XP_011513704.1
AGMO	XM_017012204.2	c.1264-27547C>A		intron_variant			XP_016867693.1
AGMO	XR_001744759.1	n.1434-27547C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33328 AN: 151936 Hom.: 3881 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.219 AC: 33353 AN: 152054 Hom.: 3884 Cov.: 33 AF XY: 0.222 AC XY: 16530 AN XY: 74334

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.217

Alfa AF: 0.200 Hom.: 4464

Bravo AF: 0.223

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6962150; hg19: chr7-15225539;