rs208747

Variant names:

• chr8-17921356-T-A
• rs208747
• XM_047422505.1:c.*1308A>T

Variant summary

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

The XM_047422505.1(LOC124901867):​c.*1308A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 152,252 control chromosomes in the GnomAD database, including 226 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 0.048 (226 hom., cov: 33)
• Consequence: LOC124901867 XM_047422505.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 4 publications found

Genes affected

LOC124901867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7327 AN: 152134 Hom.: 224 Cov.: 33

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0482 AC: 7337 AN: 152252 Hom.: 226 Cov.: 33 AF XY: 0.0496 AC XY: 3692 AN XY: 74446

African (AFR) AF: 0.0875 AC: 3634 AN: 41524

American (AMR) AF: 0.0291 AC: 445 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5186

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4826

European-Finnish (FIN) AF: 0.0615 AC: 652 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1857 AN: 68030

Other (OTH) AF: 0.0477 AC: 101 AN: 2116

Alfa AF: 0.0146 Hom.: 3

Bravo AF: 0.0459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.86
DANN	Benign	0.62
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs208747; hg19: chr8-17778865;