rs668413

chr1-109653322-C-A

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 0.395 in 152,088 control chromosomes in the GnomAD database, including 11,994 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 0.40 (11994 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 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: 0.395 AC: 60093 AN: 151968 Hom.: 11988 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.395 AC: 60138 AN: 152088 Hom.: 11994 Cov.: 33 AF XY: 0.392 AC XY: 29120 AN XY: 74336

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.379

Alfa AF: 0.407 Hom.: 16937

Bravo AF: 0.391

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.55
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs668413; hg19: chr1-110195944;