XR_007065854.1:n.1780T>G

Variant names:

• chr17-54898958-A-C
• rs8067139
• XR_007065854.1:n.1780T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC124904033 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.193 AC: 7985 AN: 41372

American (AMR) AF: 0.301 AC: 4592 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 532 AN: 3464

East Asian (EAS) AF: 0.371 AC: 1896 AN: 5112

South Asian (SAS) AF: 0.111 AC: 534 AN: 4806

European-Finnish (FIN) AF: 0.107 AC: 1126 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7935 AN: 67972

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.141 Hom.: 5052

Bravo AF: 0.186

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		0.11
PromoterAI		0.0025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8067139; hg19: chr17-52976319;