4-189616909-A-G

Variant names:

• chr4-189616909-A-G
• rs13145041

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.12 (3195 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BS2: High Homozygotes in GnomAd4 at 3195 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.123 AC: 11192 AN: 90814 Hom.: 3201 Cov.: 15

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00893

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0397

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 11179 AN: 90892 Hom.: 3195 Cov.: 15 AF XY: 0.112 AC XY: 5054 AN XY: 45034

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.111 AC: 3288 AN: 29506

American (AMR) AF: 0.0730 AC: 688 AN: 9430

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 377 AN: 1752

East Asian (EAS) AF: 0.00896 AC: 40 AN: 4466

South Asian (SAS) AF: 0.0662 AC: 197 AN: 2978

European-Finnish (FIN) AF: 0.0560 AC: 374 AN: 6678

Middle Eastern (MID) AF: 0.0328 AC: 4 AN: 122

European-Non Finnish (NFE) AF: 0.174 AC: 6006 AN: 34492

Other (OTH) AF: 0.108 AC: 117 AN: 1084

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	7.8
DANN	Benign	0.035
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs13145041; hg19: chr4-190538063;