chr4-60090806-A-G

Variant names:

• chr4-60090806-A-G
• rs10050211

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 0.19 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.189 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

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0921

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.181

Alfa AF: 0.132 Hom.: 755

Bravo AF: 0.197

Asia WGS AF: 0.380 AC: 1308 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10050211; hg19: chr4-60956524;