rs6010044

Variant names:

• chr22-50663510-A-C
• rs6010044

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 0.203 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
• Publications: 11 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.131 AC: 5457 AN: 41540

American (AMR) AF: 0.235 AC: 3602 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2225 AN: 5176

South Asian (SAS) AF: 0.245 AC: 1183 AN: 4834

European-Finnish (FIN) AF: 0.322 AC: 3404 AN: 10576

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13969 AN: 67986

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.205 Hom.: 7191

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
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs6010044; hg19: chr22-51101938;