4-60090806-A-G

Variant names:

• chr4-60090806-A-G
• rs10050211

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 0.19 in 151,520 control chromosomes in the GnomAD database, including 3,740 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 0.19 (3740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28676 AN: 151408 Hom.: 3724 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0921

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.190 AC: 28714 AN: 151520 Hom.: 3740 Cov.: 32 AF XY: 0.193 AC XY: 14324 AN XY: 74044

African (AFR) AF: 0.335 AC: 13858 AN: 41326

American (AMR) AF: 0.163 AC: 2479 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 319 AN: 3462

East Asian (EAS) AF: 0.386 AC: 1997 AN: 5176

South Asian (SAS) AF: 0.290 AC: 1400 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1273 AN: 10388

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6843 AN: 67840

Other (OTH) AF: 0.181 AC: 381 AN: 2104

Alfa AF: 0.131 Hom.: 824

Bravo AF: 0.197

Asia WGS AF: 0.380 AC: 1308 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.34
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10050211; hg19: chr4-60956524;