4-45180510-A-G

Variant names:

• chr4-45180510-A-G
• rs10938397

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 0.374 in 151,772 control chromosomes in the GnomAD database, including 11,281 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 0.37 (11281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 342 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56777 AN: 151654 Hom.: 11280 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.374 AC: 56787 AN: 151772 Hom.: 11281 Cov.: 32 AF XY: 0.376 AC XY: 27916 AN XY: 74186

African (AFR) AF: 0.242 AC: 10022 AN: 41426

American (AMR) AF: 0.404 AC: 6159 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3466

East Asian (EAS) AF: 0.282 AC: 1461 AN: 5172

South Asian (SAS) AF: 0.391 AC: 1884 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5310 AN: 10538

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.431 AC: 29218 AN: 67812

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.414 Hom.: 37432

Bravo AF: 0.361

Asia WGS AF: 0.302 AC: 1049 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10938397; hg19: chr4-45182527;