rs6007413

Variant names:

• chr22-45034435-C-G
• rs6007413

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 0.177 in 152,152 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.177 AC: 26925 AN: 152034 Hom.: 2611 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.177 AC: 26971 AN: 152152 Hom.: 2621 Cov.: 32 AF XY: 0.184 AC XY: 13674 AN XY: 74378

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.175

Alfa AF: 0.153 Hom.: 238

Bravo AF: 0.181

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6007413; hg19: chr22-45430316;