chr8-38584525-G-A

Variant names:

• chr8-38584525-G-A
• rs16887478
• XR_007060891.1:n.8908G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060891.1(LOC105379384):​n.8908G>A 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 0.135 in 152,106 control chromosomes in the GnomAD database, including 1,477 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 0.14 (1477 hom., cov: 33)
• Consequence: LOC105379384 XR_007060891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 3 publications found

Genes affected

LOC105379384 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 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: 0.135 AC: 20549 AN: 151988 Hom.: 1475 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.135 AC: 20565 AN: 152106 Hom.: 1477 Cov.: 33 AF XY: 0.133 AC XY: 9901 AN XY: 74356

African (AFR) AF: 0.133 AC: 5509 AN: 41498

American (AMR) AF: 0.141 AC: 2150 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3468

East Asian (EAS) AF: 0.0886 AC: 459 AN: 5178

South Asian (SAS) AF: 0.117 AC: 566 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9476 AN: 67974

Other (OTH) AF: 0.135 AC: 285 AN: 2110

Alfa AF: 0.134 Hom.: 522

Bravo AF: 0.139

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.28
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs16887478; hg19: chr8-38442043;