rs904276

Variant names:

• chr18-53907970-T-C
• rs904276

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.234 AC: 9687 AN: 41478

American (AMR) AF: 0.186 AC: 2841 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.0487 AC: 252 AN: 5178

South Asian (SAS) AF: 0.204 AC: 985 AN: 4828

European-Finnish (FIN) AF: 0.241 AC: 2551 AN: 10580

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16311 AN: 67978

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.221 Hom.: 601

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs904276; hg19: chr18-51434340;