rs168924

Positions:

• chr16-55655632-A-G

Variant summary

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

The XR_007065075.1(LOC124903693):​n.482T>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 0.157 in 152,320 control chromosomes in the GnomAD database, including 2,017 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 0.16 (2016 hom., cov: 33)
  • Exomes 𝑓: 0.085 (1 hom.)
• Consequence: LOC124903693 XR_007065075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

Genes affected

LOC124903693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903693	XR_007065075.1	n.482T>C		non_coding_transcript_exon_variant	1/2
		n.55655632A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23852 AN: 152108 Hom.: 2015 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.0851 AC: 8 AN: 94 Hom.: 1 Cov.: 0 AF XY: 0.0811 AC XY: 6 AN XY: 74

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.0946

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.157 AC: 23876 AN: 152226 Hom.: 2016 Cov.: 33 AF XY: 0.155 AC XY: 11507 AN XY: 74440

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.149

Alfa AF: 0.147 Hom.: 1644

Bravo AF: 0.161

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs168924; hg19: chr16-55689544;