rs10013228

Variant names:

• chr4-55131173-A-G
• rs10013228

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 0.228 in 152,136 control chromosomes in the GnomAD database, including 4,279 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 0.23 (4279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34690 AN: 152018 Hom.: 4281 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.228 AC: 34684 AN: 152136 Hom.: 4279 Cov.: 32 AF XY: 0.226 AC XY: 16839 AN XY: 74376

African (AFR) AF: 0.144 AC: 5993 AN: 41496

American (AMR) AF: 0.208 AC: 3178 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.179 AC: 926 AN: 5186

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4814

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10576

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18847 AN: 67986

Other (OTH) AF: 0.241 AC: 511 AN: 2116

Alfa AF: 0.262 Hom.: 16294

Bravo AF: 0.222

Asia WGS AF: 0.194 AC: 673 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10013228; hg19: chr4-55997340;