rs10033854

Variant names:

• chr4-69654186-G-A
• rs10033854

Your query was ambiguous. Multiple possible variants found:

• chr4-69654186-G-A
• chr4-69654186-G-C

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 0.479 in 151,810 control chromosomes in the GnomAD database, including 17,629 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 0.48 (17629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.479 AC: 72610 AN: 151692 Hom.: 17622 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.479 AC: 72651 AN: 151810 Hom.: 17629 Cov.: 32 AF XY: 0.475 AC XY: 35207 AN XY: 74184

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.499

Alfa AF: 0.479 Hom.: 29655

Bravo AF: 0.482

Asia WGS AF: 0.598 AC: 2078 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	1.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10033854; hg19: chr4-70519904;