chr4-89323325-C-A

Variant names:

• chr4-89323325-C-A
• rs4106153

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.888 AC: 36867 AN: 41504

American (AMR) AF: 0.744 AC: 11365 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2613 AN: 5166

South Asian (SAS) AF: 0.736 AC: 3548 AN: 4820

European-Finnish (FIN) AF: 0.746 AC: 7875 AN: 10554

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.803 AC: 54575 AN: 68004

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.798 Hom.: 191207

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4106153; hg19: chr4-90244476;