rs903146

Variant names:

• chr8-54913836-T-C
• rs903146

Variant summary

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

The variant allele was found at a frequency of 0.383 in 152,000 control chromosomes in the GnomAD database, including 12,982 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 0.38 (12982 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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 (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58140 AN: 151884 Hom.: 12943 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.383 AC: 58235 AN: 152000 Hom.: 12982 Cov.: 31 AF XY: 0.375 AC XY: 27881 AN XY: 74328

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.367

Alfa AF: 0.348 Hom.: 1761

Bravo AF: 0.395

Asia WGS AF: 0.248 AC: 860 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903146; hg19: chr8-55826396;