rs4399277

Variant names:

• chr10-80121266-G-A
• rs4399277

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 0.0873 in 152,118 control chromosomes in the GnomAD database, including 656 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 0.087 (656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 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: 0.0872 AC: 13254 AN: 152000 Hom.: 649 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0672

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0873 AC: 13284 AN: 152118 Hom.: 656 Cov.: 33 AF XY: 0.0867 AC XY: 6451 AN XY: 74386

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0268

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0967 Hom.: 117

Bravo AF: 0.0825

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4399277; hg19: chr10-81881022;