4-45366129-A-T

Variant names:

• chr4-45366129-A-T
• rs10517134

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 0.896 in 152,232 control chromosomes in the GnomAD database, including 61,504 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 0.90 (61504 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.955 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: 0.896 AC: 136302 AN: 152114 Hom.: 61479 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.896 AC: 136369 AN: 152232 Hom.: 61504 Cov.: 33 AF XY: 0.898 AC XY: 66829 AN XY: 74438

African (AFR) AF: 0.785 AC: 32567 AN: 41508

American (AMR) AF: 0.923 AC: 14119 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3190 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5060 AN: 5174

South Asian (SAS) AF: 0.863 AC: 4168 AN: 4828

European-Finnish (FIN) AF: 0.956 AC: 10141 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64021 AN: 68028

Other (OTH) AF: 0.914 AC: 1935 AN: 2116

Alfa AF: 0.901 Hom.: 3487

Bravo AF: 0.891

Asia WGS AF: 0.901 AC: 3134 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	0.66
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10517134; hg19: chr4-45368146;