rs4466940

Variant names:

• chr13-30767140-C-T
• rs4466940

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 0.207 in 152,068 control chromosomes in the GnomAD database, including 3,307 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 0.21 (3307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.277 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: 0.207 AC: 31528 AN: 151948 Hom.: 3308 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.207 AC: 31528 AN: 152068 Hom.: 3307 Cov.: 32 AF XY: 0.208 AC XY: 15468 AN XY: 74336

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.198

Alfa AF: 0.206 Hom.: 392

Bravo AF: 0.202

Asia WGS AF: 0.235 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4466940; hg19: chr13-31341277;