rs668413

Variant names:

• chr1-109653322-C-A
• rs668413

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 0.395 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
• Publications: 13 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.399 AC: 16542 AN: 41468

American (AMR) AF: 0.319 AC: 4884 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1269 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1601 AN: 5178

South Asian (SAS) AF: 0.449 AC: 2167 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3688 AN: 10552

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.420 AC: 28566 AN: 67986

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.405 Hom.: 21433

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs668413; hg19: chr1-110195944;