rs4388822

Variant names:

• chr10-84886735-C-T
• rs4388822

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 0.954 in 152,172 control chromosomes in the GnomAD database, including 69,309 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 0.95 (69309 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 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: 0.954 AC: 145024 AN: 152054 Hom.: 69251 Cov.: 30

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.954 AC: 145141 AN: 152172 Hom.: 69309 Cov.: 30 AF XY: 0.953 AC XY: 70855 AN XY: 74370

Gnomad4 AFR AF: 0.990

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.965

Alfa AF: 0.940 Hom.: 32474

Bravo AF: 0.962

Asia WGS AF: 0.989 AC: 3440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4388822; hg19: chr10-86646491;