rs903146

Positions:

• chr8-54913836-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;