rs12934552

chr16-56987521-A-G

Variant summary

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

The XR_007065081.1(LOC124903696):n.1632T>C 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 0.112 in 152,190 control chromosomes in the GnomAD database, including 1,055 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 0.11 (1055 hom., cov: 32)
• Consequence: LOC124903696 XR_007065081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

LOC124903696 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903696	XR_007065081.1	n.1632T>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16991 AN: 152072 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.112 AC: 16999 AN: 152190 Hom.: 1055 Cov.: 32 AF XY: 0.107 AC XY: 7959 AN XY: 74410

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.107

Alfa AF: 0.128 Hom.: 1843

Bravo AF: 0.111

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12934552; hg19: chr16-57021433;