rs8067139

chr17-54898958-A-C

Variant summary

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

The XR_007065854.1(LOC124904033):n.1780T>G 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 0.165 in 151,864 control chromosomes in the GnomAD database, including 2,556 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 0.17 (2556 hom., cov: 30)
• Consequence: LOC124904033 XR_007065854.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

Genes affected

LOC124904033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904033	XR_007065854.1	n.1780T>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25065 AN: 151746 Hom.: 2552 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.165 AC: 25096 AN: 151864 Hom.: 2556 Cov.: 30 AF XY: 0.166 AC XY: 12353 AN XY: 74230

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.145

Alfa AF: 0.132 Hom.: 2648

Bravo AF: 0.186

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
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: rs8067139; hg19: chr17-52976319;