4-18044876-A-G

Variant names:

• chr4-18044876-A-G
• rs1325107

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 0.695 in 151,978 control chromosomes in the GnomAD database, including 36,734 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 0.69 (36734 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105509 AN: 151860 Hom.: 36690 Cov.: 30

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.695 AC: 105602 AN: 151978 Hom.: 36734 Cov.: 30 AF XY: 0.693 AC XY: 51510 AN XY: 74300

African (AFR) AF: 0.696 AC: 28862 AN: 41446

American (AMR) AF: 0.644 AC: 9834 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2560 AN: 3466

East Asian (EAS) AF: 0.561 AC: 2896 AN: 5160

South Asian (SAS) AF: 0.850 AC: 4088 AN: 4808

European-Finnish (FIN) AF: 0.706 AC: 7461 AN: 10570

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47647 AN: 67956

Other (OTH) AF: 0.689 AC: 1449 AN: 2104

Alfa AF: 0.710 Hom.: 22086

Bravo AF: 0.685

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1325107; hg19: chr4-18046499;