rs904276

chr18-53907970-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 0.227 in 152,116 control chromosomes in the GnomAD database, including 4,082 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 0.23 (4082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34509 AN: 151998 Hom.: 4078 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.227 AC: 34531 AN: 152116 Hom.: 4082 Cov.: 32 AF XY: 0.225 AC XY: 16765 AN XY: 74370

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.226

Alfa AF: 0.220 Hom.: 572

Bravo AF: 0.221

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.012
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904276; hg19: chr18-51434340;