chr4-189616909-A-C

Variant names:

• chr4-189616909-A-C
• rs13145041

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.13 (3863 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

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: 0.132 AC: 12263 AN: 93094 Hom.: 3854 Cov.: 15

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.0859

Gnomad NFE AF: 0.00690

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.132 AC: 12294 AN: 93176 Hom.: 3863 Cov.: 15 AF XY: 0.143 AC XY: 6608 AN XY: 46128

African (AFR) AF: 0.190 AC: 5741 AN: 30254

American (AMR) AF: 0.319 AC: 3078 AN: 9642

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 173 AN: 1810

East Asian (EAS) AF: 0.464 AC: 2098 AN: 4524

South Asian (SAS) AF: 0.0562 AC: 172 AN: 3060

European-Finnish (FIN) AF: 0.0941 AC: 637 AN: 6766

Middle Eastern (MID) AF: 0.0887 AC: 11 AN: 124

European-Non Finnish (NFE) AF: 0.00690 AC: 245 AN: 35496

Other (OTH) AF: 0.125 AC: 139 AN: 1108

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	7.5
DANN	Benign	0.065
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;