rs6010044

Positions:

• chr22-50663510-A-C

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 0.203 in 152,202 control chromosomes in the GnomAD database, including 3,546 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 0.20 (3546 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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: 0.203 AC: 30925 AN: 152084 Hom.: 3536 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.203 AC: 30967 AN: 152202 Hom.: 3546 Cov.: 33 AF XY: 0.211 AC XY: 15727 AN XY: 74410

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.192

Alfa AF: 0.204 Hom.: 1805

Bravo AF: 0.194

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6010044; hg19: chr22-51101938;