rs208747

chr8-17921356-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901867 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901867	XM_047422505.1	c.*1308A>T		3_prime_UTR_variant	4/4

Ensembl

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

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

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0580

Gnomad4 FIN AF: 0.0615

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0477

Alfa AF: 0.0146 Hom.: 3

Bravo AF: 0.0459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.86
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208747; hg19: chr8-17778865;