rs4106153

Variant names:

• chr4-89323325-C-A
• rs4106153

Your query was ambiguous. Multiple possible variants found:

• chr4-89323325-C-A
• chr4-89323325-C-G

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 0.803 in 152,106 control chromosomes in the GnomAD database, including 49,514 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 0.80 (49514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.803 AC: 122080 AN: 151988 Hom.: 49478 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.803 AC: 122163 AN: 152106 Hom.: 49514 Cov.: 32 AF XY: 0.798 AC XY: 59321 AN XY: 74352

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.785

Alfa AF: 0.794 Hom.: 85036

Bravo AF: 0.804

Asia WGS AF: 0.661 AC: 2299 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	0.13
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4106153; hg19: chr4-90244476;